OSCR

<i>Drosophila</i> RSK: A Pivotal Regulator of Circadian Plasticity at the Neuronal and Behavioral Level.

Code ↔ Paper

1 match between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 1 match
  1. [1] § Materials and Methods › Quantification of s-LNv Arborization ↔ src/MorphoScope.py, lines 532–575 · score 0.63 · graphical user interface, MorphoScope, dimensions, quantify

Paper

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The authors' code

Python · 2,304 lines · 91 KB · MIT · 1 match

  1. """
  2. MorphoScope - Main Window Implementation
  4. This module contains the main window class for the MorphoScope application,
  5. a tool for quantifying structural plasticity in 3D microscopy images of
  6. neuronal projections.
  8. Features:
  9. - Multi-format image loading (CZI, TIF, LSM)
  10. - Interactive ROI selection
  11. - Image filtering and preprocessing
  12. - Structural plasticity quantification
  13. - Batch processing and CSV export
  15. Author: Francisco Tassara
  16. Date: 2025-11-12
  17. Based on: Petsakou, Sapsis & Blau, Cell 2015
  18. """
  21. from PySide6.QtCore import (QCoreApplication, QDate, QDateTime, QLocale,
  22. QMetaObject, QObject, QPoint, QRect,
  23. QSize, QTime, QUrl, Qt)
  24. from PySide6.QtGui import (QBrush, QColor, QConicalGradient, QCursor,
  25. QFont, QFontDatabase, QGradient, QIcon,
  26. QImage, QKeySequence, QLinearGradient, QPainter,
  27. QPalette, QPixmap, QRadialGradient, QTransform)
  28. from PySide6.QtWidgets import (QApplication, QComboBox, QGroupBox, QHBoxLayout,
  29. QLabel, QLayout, QLineEdit, QListWidget, QCheckBox,
  30. QListWidgetItem, QMainWindow, QPushButton, QRadioButton,
  31. QSizePolicy, QSpacerItem, QSpinBox, QTextEdit,
  32. QVBoxLayout, QWidget, QProgressDialog)
  34. from pyqtgraph import ImageView
  35. import pyqtgraph
  37. from PySide6.QtWidgets import QMessageBox, QFileDialog, QInputDialog
  38. import sys
  39. import os
  40. import numpy as np
  41. from matplotlib.path import Path as MPLPath
  42. from scipy import ndimage as ndi
  43. from shapely.geometry import Polygon
  45. import csv
  46. import matplotlib.pyplot as plt
  48. import tifffile
  49. from pylibCZIrw import czi
  51. from scipy.ndimage import median_filter
  52. from skimage.filters import gaussian
  54. from config import Config, setup_logging
  55. from image_processor import ImageProcessor, validate_parameters
  57. from typing import Optional, Tuple, List
  59. # Configurar logging
  60. import logging
  61. setup_logging()
  62. logger = logging.getLogger(__name__)
  64. class Ui_MainWindow(object):
  65. def setupUi(self, MainWindow):
  66. if not MainWindow.objectName():
  67. MainWindow.setObjectName(u"MainWindow")
  68. MainWindow.resize(1316, 815)
  69. icon = QIcon()
  70. icon.addFile(u"logo.ico", QSize(), QIcon.Mode.Normal, QIcon.State.Off)
  71. MainWindow.setWindowIcon(icon)
  72. self.centralwidget = QWidget(MainWindow)
  73. self.centralwidget.setObjectName(u"centralwidget")
  74. self.horizontalLayout_10 = QHBoxLayout(self.centralwidget)
  75. self.horizontalLayout_10.setObjectName(u"horizontalLayout_10")
  76. self.verticalLayout_11 = QVBoxLayout()
  77. self.verticalLayout_11.setObjectName(u"verticalLayout_11")
  78. self.horizontalLayout_7 = QHBoxLayout()
  79. self.horizontalLayout_7.setObjectName(u"horizontalLayout_7")
  80. self.pushButton_loadImage = QPushButton(self.centralwidget)
  81. self.pushButton_loadImage.setObjectName(u"pushButton_loadImage")
  82. font = QFont()
  83. font.setPointSize(10)
  84. font.setBold(True)
  85. self.pushButton_loadImage.setFont(font)
  87. self.horizontalLayout_7.addWidget(self.pushButton_loadImage)
  89. self.pushButton_clean = QPushButton(self.centralwidget)
  90. self.pushButton_clean.setObjectName(u"pushButton_clean")
  91. font1 = QFont()
  92. font1.setPointSize(10)
  93. self.pushButton_clean.setFont(font1)
  95. self.horizontalLayout_7.addWidget(self.pushButton_clean)
  98. self.verticalLayout_11.addLayout(self.horizontalLayout_7)
  100. self.listWidget_images = QListWidget(self.centralwidget)
  101. self.listWidget_images.setObjectName(u"listWidget_images")
  103. self.verticalLayout_11.addWidget(self.listWidget_images)
  105. self.groupBox_properties = QGroupBox(self.centralwidget)
  106. self.groupBox_properties.setObjectName(u"groupBox_properties")
  107. self.groupBox_properties.setFont(font1)
  108. self.horizontalLayout = QHBoxLayout(self.groupBox_properties)
  109. self.horizontalLayout.setObjectName(u"horizontalLayout")
  110. self.verticalLayout_10 = QVBoxLayout()
  111. self.verticalLayout_10.setObjectName(u"verticalLayout_10")
  112. self.label_5 = QLabel(self.groupBox_properties)
  113. self.label_5.setObjectName(u"label_5")
  115. self.verticalLayout_10.addWidget(self.label_5)
  117. self.label_2 = QLabel(self.groupBox_properties)
  118. self.label_2.setObjectName(u"label_2")
  120. self.verticalLayout_10.addWidget(self.label_2)
  123. self.horizontalLayout.addLayout(self.verticalLayout_10)
  125. self.verticalLayout_3 = QVBoxLayout()
  126. self.verticalLayout_3.setObjectName(u"verticalLayout_3")
  127. self.lineEdit_image_size_X = QLineEdit(self.groupBox_properties)
  128. self.lineEdit_image_size_X.setObjectName(u"lineEdit_image_size_X")
  130. self.verticalLayout_3.addWidget(self.lineEdit_image_size_X)
  132. self.lineEdit_pixel_size_X = QLineEdit(self.groupBox_properties)
  133. self.lineEdit_pixel_size_X.setObjectName(u"lineEdit_pixel_size_X")
  135. self.verticalLayout_3.addWidget(self.lineEdit_pixel_size_X)
  138. self.horizontalLayout.addLayout(self.verticalLayout_3)
  140. self.verticalLayout_5 = QVBoxLayout()
  141. self.verticalLayout_5.setObjectName(u"verticalLayout_5")
  142. self.label_6 = QLabel(self.groupBox_properties)
  143. self.label_6.setObjectName(u"label_6")
  145. self.verticalLayout_5.addWidget(self.label_6)
  147. self.label_9 = QLabel(self.groupBox_properties)
  148. self.label_9.setObjectName(u"label_9")
  150. self.verticalLayout_5.addWidget(self.label_9)
  153. self.horizontalLayout.addLayout(self.verticalLayout_5)
  155. self.verticalLayout_6 = QVBoxLayout()
  156. self.verticalLayout_6.setObjectName(u"verticalLayout_6")
  157. self.lineEdit_image_size_Y = QLineEdit(self.groupBox_properties)
  158. self.lineEdit_image_size_Y.setObjectName(u"lineEdit_image_size_Y")
  160. self.verticalLayout_6.addWidget(self.lineEdit_image_size_Y)
  162. self.lineEdit_pixel_size_Y = QLineEdit(self.groupBox_properties)
  163. self.lineEdit_pixel_size_Y.setObjectName(u"lineEdit_pixel_size_Y")
  165. self.verticalLayout_6.addWidget(self.lineEdit_pixel_size_Y)
  168. self.horizontalLayout.addLayout(self.verticalLayout_6)
  170. self.verticalLayout_7 = QVBoxLayout()
  171. self.verticalLayout_7.setObjectName(u"verticalLayout_7")
  172. self.label_7 = QLabel(self.groupBox_properties)
  173. self.label_7.setObjectName(u"label_7")
  175. self.verticalLayout_7.addWidget(self.label_7)
  177. self.label_10 = QLabel(self.groupBox_properties)
  178. self.label_10.setObjectName(u"label_10")
  180. self.verticalLayout_7.addWidget(self.label_10)
  183. self.horizontalLayout.addLayout(self.verticalLayout_7)
  185. self.verticalLayout_8 = QVBoxLayout()
  186. self.verticalLayout_8.setObjectName(u"verticalLayout_8")
  187. self.lineEdit_image_size_Z = QLineEdit(self.groupBox_properties)
  188. self.lineEdit_image_size_Z.setObjectName(u"lineEdit_image_size_Z")
  190. self.verticalLayout_8.addWidget(self.lineEdit_image_size_Z)
  192. self.lineEdit_pixel_size_Z = QLineEdit(self.groupBox_properties)
  193. self.lineEdit_pixel_size_Z.setObjectName(u"lineEdit_pixel_size_Z")
  195. self.verticalLayout_8.addWidget(self.lineEdit_pixel_size_Z)
  198. self.horizontalLayout.addLayout(self.verticalLayout_8)
  200. self.verticalLayout_9 = QVBoxLayout()
  201. self.verticalLayout_9.setObjectName(u"verticalLayout_9")
  202. self.label_8 = QLabel(self.groupBox_properties)
  203. self.label_8.setObjectName(u"label_8")
  205. self.verticalLayout_9.addWidget(self.label_8)
  207. self.label_11 = QLabel(self.groupBox_properties)
  208. self.label_11.setObjectName(u"label_11")
  210. self.verticalLayout_9.addWidget(self.label_11)
  213. self.horizontalLayout.addLayout(self.verticalLayout_9)
  216. self.verticalLayout_11.addWidget(self.groupBox_properties)
  218. self.groupBox_visualizer = QGroupBox(self.centralwidget)
  219. self.groupBox_visualizer.setObjectName(u"groupBox_visualizer")
  220. self.groupBox_visualizer.setFont(font1)
  221. self.verticalLayout = QVBoxLayout(self.groupBox_visualizer)
  222. self.verticalLayout.setObjectName(u"verticalLayout")
  223. self.horizontalLayout_4 = QHBoxLayout()
  224. self.horizontalLayout_4.setObjectName(u"horizontalLayout_4")
  225. self.label_4 = QLabel(self.groupBox_visualizer)
  226. self.label_4.setObjectName(u"label_4")
  228. self.horizontalLayout_4.addWidget(self.label_4)
  230. self.comboBox_channel_selector = QComboBox(self.groupBox_visualizer)
  231. self.comboBox_channel_selector.setObjectName(u"comboBox_channel_selector")
  233. self.horizontalLayout_4.addWidget(self.comboBox_channel_selector)
  236. self.verticalLayout.addLayout(self.horizontalLayout_4)
  238. self.horizontalLayout_6 = QHBoxLayout()
  239. self.horizontalLayout_6.setObjectName(u"horizontalLayout_6")
  240. self.label_12 = QLabel(self.groupBox_visualizer)
  241. self.label_12.setObjectName(u"label_12")
  243. self.horizontalLayout_6.addWidget(self.label_12)
  245. self.radioButton_plotZproject = QRadioButton(self.groupBox_visualizer)
  246. self.radioButton_plotZproject.setObjectName(u"radioButton_plotZproject")
  247. self.radioButton_plotZproject.setChecked(True)
  249. self.horizontalLayout_6.addWidget(self.radioButton_plotZproject)
  251. self.radioButton_plotStack = QRadioButton(self.groupBox_visualizer)
  252. self.radioButton_plotStack.setObjectName(u"radioButton_plotStack")
  254. self.horizontalLayout_6.addWidget(self.radioButton_plotStack)
  257. self.verticalLayout.addLayout(self.horizontalLayout_6)
  260. self.verticalLayout_11.addWidget(self.groupBox_visualizer)
  262. self.groupBox_channels = QGroupBox(self.centralwidget)
  263. self.groupBox_channels.setObjectName(u"groupBox_channels")
  264. font2 = QFont()
  265. font2.setPointSize(10)
  266. font2.setBold(False)
  267. self.groupBox_channels.setFont(font2)
  268. self.verticalLayout_2 = QVBoxLayout(self.groupBox_channels)
  269. self.verticalLayout_2.setObjectName(u"verticalLayout_2")
  270. self.horizontalLayout_2 = QHBoxLayout()
  271. self.horizontalLayout_2.setSpacing(1)
  272. self.horizontalLayout_2.setObjectName(u"horizontalLayout_2")
  273. self.label = QLabel(self.groupBox_channels)
  274. self.label.setObjectName(u"label")
  276. self.horizontalLayout_2.addWidget(self.label)
  278. self.comboBox_plasticityChannel = QComboBox(self.groupBox_channels)
  279. self.comboBox_plasticityChannel.setObjectName(u"comboBox_plasticityChannel")
  281. self.horizontalLayout_2.addWidget(self.comboBox_plasticityChannel)
  283. self.comboBox_filter_type_chP = QComboBox(self.groupBox_channels)
  284. self.comboBox_filter_type_chP.addItem("")
  285. self.comboBox_filter_type_chP.addItem("")
  286. self.comboBox_filter_type_chP.addItem("")
  287. self.comboBox_filter_type_chP.addItem("")
  288. self.comboBox_filter_type_chP.addItem("")
  289. self.comboBox_filter_type_chP.setObjectName(u"comboBox_filter_type_chP")
  291. self.horizontalLayout_2.addWidget(self.comboBox_filter_type_chP)
  293. self.pushButton_applyfilter_chP = QPushButton(self.groupBox_channels)
  294. self.pushButton_applyfilter_chP.setObjectName(u"pushButton_applyfilter_chP")
  296. self.horizontalLayout_2.addWidget(self.pushButton_applyfilter_chP)
  298. self.pushButton_undofilter_chP = QPushButton(self.groupBox_channels)
  299. self.pushButton_undofilter_chP.setObjectName(u"pushButton_undofilter_chP")
  301. self.horizontalLayout_2.addWidget(self.pushButton_undofilter_chP)
  303. self.horizontalLayout_2.setStretch(0, 1)
  304. self.horizontalLayout_2.setStretch(1, 5)
  305. self.horizontalLayout_2.setStretch(2, 1)
  306. self.horizontalLayout_2.setStretch(3, 1)
  307. self.horizontalLayout_2.setStretch(4, 1)
  309. self.verticalLayout_2.addLayout(self.horizontalLayout_2)
  311. self.horizontalLayout_3 = QHBoxLayout()
  312. self.horizontalLayout_3.setSpacing(1)
  313. self.horizontalLayout_3.setObjectName(u"horizontalLayout_3")
  314. self.horizontalLayout_3.setSizeConstraint(QLayout.SizeConstraint.SetDefaultConstraint)
  315. self.label_3 = QLabel(self.groupBox_channels)
  316. self.label_3.setObjectName(u"label_3")
  318. self.horizontalLayout_3.addWidget(self.label_3)
  320. self.comboBox_fluoChannel = QComboBox(self.groupBox_channels)
  321. self.comboBox_fluoChannel.setObjectName(u"comboBox_fluoChannel")
  323. self.horizontalLayout_3.addWidget(self.comboBox_fluoChannel)
  325. self.comboBox_filter_type_chF = QComboBox(self.groupBox_channels)
  326. self.comboBox_filter_type_chF.addItem("")
  327. self.comboBox_filter_type_chF.addItem("")
  328. self.comboBox_filter_type_chF.addItem("")
  329. self.comboBox_filter_type_chF.addItem("")
  330. self.comboBox_filter_type_chF.addItem("")
  331. self.comboBox_filter_type_chF.setObjectName(u"comboBox_filter_type_chF")
  333. self.horizontalLayout_3.addWidget(self.comboBox_filter_type_chF)
  335. self.pushButton_applyfilter_chF = QPushButton(self.groupBox_channels)
  336. self.pushButton_applyfilter_chF.setObjectName(u"pushButton_applyfilter_chF")
  338. self.horizontalLayout_3.addWidget(self.pushButton_applyfilter_chF)
  340. self.pushButton_undofilter_chF = QPushButton(self.groupBox_channels)
  341. self.pushButton_undofilter_chF.setObjectName(u"pushButton_undofilter_chF")
  343. self.horizontalLayout_3.addWidget(self.pushButton_undofilter_chF)
  345. self.horizontalLayout_3.setStretch(0, 1)
  346. self.horizontalLayout_3.setStretch(1, 5)
  347. self.horizontalLayout_3.setStretch(2, 1)
  348. self.horizontalLayout_3.setStretch(3, 1)
  349. self.horizontalLayout_3.setStretch(4, 1)
  351. self.verticalLayout_2.addLayout(self.horizontalLayout_3)
  354. self.verticalLayout_11.addWidget(self.groupBox_channels)
  356. self.groupBox_observations = QGroupBox(self.centralwidget)
  357. self.groupBox_observations.setObjectName(u"groupBox_observations")
  358. self.groupBox_observations.setFont(font1)
  359. self.verticalLayout_4 = QVBoxLayout(self.groupBox_observations)
  360. self.verticalLayout_4.setObjectName(u"verticalLayout_4")
  361. self.textEdit_observation = QTextEdit(self.groupBox_observations)
  362. self.textEdit_observation.setObjectName(u"textEdit_observation")
  363. self.textEdit_observation.setFont(font1)
  365. self.verticalLayout_4.addWidget(self.textEdit_observation)
  368. self.verticalLayout_11.addWidget(self.groupBox_observations)
  370. self.groupBox_roi = QGroupBox(self.centralwidget)
  371. self.groupBox_roi.setObjectName(u"groupBox_roi")
  372. self.groupBox_roi.setFont(font1)
  373. self.horizontalLayout_5 = QHBoxLayout(self.groupBox_roi)
  374. self.horizontalLayout_5.setObjectName(u"horizontalLayout_5")
  375. self.pushButton_roi = QPushButton(self.groupBox_roi)
  376. self.pushButton_roi.setObjectName(u"pushButton_roi")
  377. self.pushButton_roi.setFont(font1)
  379. self.horizontalLayout_5.addWidget(self.pushButton_roi)
  381. self.pushButton_apply_roi = QPushButton(self.groupBox_roi)
  382. self.pushButton_apply_roi.setObjectName(u"pushButton_apply_roi")
  383. self.pushButton_apply_roi.setFont(font1)
  385. self.horizontalLayout_5.addWidget(self.pushButton_apply_roi)
  388. self.verticalLayout_11.addWidget(self.groupBox_roi)
  390. self.horizontalLayout_8 = QHBoxLayout()
  391. self.horizontalLayout_8.setObjectName(u"horizontalLayout_8")
  392. self.groupBox = QGroupBox(self.centralwidget)
  393. self.groupBox.setObjectName(u"groupBox")
  394. self.groupBox.setFont(font1)
  395. self.horizontalLayout_9 = QHBoxLayout(self.groupBox)
  396. self.horizontalLayout_9.setObjectName(u"horizontalLayout_9")
  397. self.horizontalLayout_9.setContentsMargins(-1, -1, -1, 3)
  398. self.label_13 = QLabel(self.groupBox)
  399. self.label_13.setObjectName(u"label_13")
  401. self.horizontalLayout_9.addWidget(self.label_13)
  403. self.spinBox_zmin = QSpinBox(self.groupBox)
  404. self.spinBox_zmin.setObjectName(u"spinBox_zmin")
  406. self.horizontalLayout_9.addWidget(self.spinBox_zmin)
  408. self.horizontalSpacer_2 = QSpacerItem(40, 20, QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Minimum)
  410. self.horizontalLayout_9.addItem(self.horizontalSpacer_2)
  412. self.label_14 = QLabel(self.groupBox)
  413. self.label_14.setObjectName(u"label_14")
  415. self.horizontalLayout_9.addWidget(self.label_14)
  417. self.spinBox_zmax = QSpinBox(self.groupBox)
  418. self.spinBox_zmax.setObjectName(u"spinBox_zmax")
  420. self.horizontalLayout_9.addWidget(self.spinBox_zmax)
  422. self.horizontalLayout_9.setStretch(0, 1)
  423. self.horizontalLayout_9.setStretch(1, 1)
  424. self.horizontalLayout_9.setStretch(2, 4)
  425. self.horizontalLayout_9.setStretch(3, 1)
  426. self.horizontalLayout_9.setStretch(4, 1)
  428. self.horizontalLayout_8.addWidget(self.groupBox)
  430. self.checkBox_show_distributions = QCheckBox(self.centralwidget)
  431. self.checkBox_show_distributions.setObjectName(u"checkBox_show_distributions")
  433. self.horizontalLayout_8.addWidget(self.checkBox_show_distributions)
  436. self.verticalLayout_11.addLayout(self.horizontalLayout_8)
  438. self.pushButton_procces = QPushButton(self.centralwidget)
  439. self.pushButton_procces.setObjectName(u"pushButton_procces")
  440. font3 = QFont()
  441. font3.setPointSize(12)
  442. font3.setBold(True)
  443. self.pushButton_procces.setFont(font3)
  445. self.verticalLayout_11.addWidget(self.pushButton_procces)
  447. self.verticalLayout_11.setStretch(0, 1)
  448. self.verticalLayout_11.setStretch(1, 2)
  449. self.verticalLayout_11.setStretch(2, 1)
  450. self.verticalLayout_11.setStretch(3, 1)
  451. self.verticalLayout_11.setStretch(4, 1)
  452. self.verticalLayout_11.setStretch(5, 1)
  453. self.verticalLayout_11.setStretch(6, 1)
  454. self.verticalLayout_11.setStretch(7, 1)
  455. self.verticalLayout_11.setStretch(8, 1)
  457. self.horizontalLayout_10.addLayout(self.verticalLayout_11)
  459. self.graphWidget = ImageView(self.centralwidget)
  460. self.graphWidget.setObjectName(u"graphWidget")
  461. self.graphWidget.setStyleSheet(u"background-color: rgb(0, 0, 0);")
  463. self.horizontalLayout_10.addWidget(self.graphWidget)
  465. self.horizontalLayout_10.setStretch(0, 1)
  466. self.horizontalLayout_10.setStretch(1, 2)
  467. MainWindow.setCentralWidget(self.centralwidget)
  469. self.retranslateUi(MainWindow)
  471. QMetaObject.connectSlotsByName(MainWindow)
  472. # setupUi
  474. def retranslateUi(self, MainWindow):
  475. MainWindow.setWindowTitle(QCoreApplication.translate("MainWindow", u"MorphoScope", None))
  476. self.pushButton_loadImage.setText(QCoreApplication.translate("MainWindow", u"Load images", None))
  477. self.pushButton_clean.setText(QCoreApplication.translate("MainWindow", u"Clean", None))
  478. self.groupBox_properties.setTitle(QCoreApplication.translate("MainWindow", u"Image Properties", None))
  479. self.label_5.setText(QCoreApplication.translate("MainWindow", u"Image Size (X,Y,Z):", None))
  480. self.label_2.setText(QCoreApplication.translate("MainWindow", u"Voxel Size (X,Y,Z):", None))
  481. self.lineEdit_image_size_X.setText(QCoreApplication.translate("MainWindow", u"X", None))
  482. self.lineEdit_pixel_size_X.setText(QCoreApplication.translate("MainWindow", u"X", None))
  483. self.label_6.setText(QCoreApplication.translate("MainWindow", u"x", None))
  484. self.label_9.setText(QCoreApplication.translate("MainWindow", u"x", None))
  485. self.lineEdit_image_size_Y.setText(QCoreApplication.translate("MainWindow", u"Y", None))
  486. self.lineEdit_pixel_size_Y.setText(QCoreApplication.translate("MainWindow", u"Y", None))
  487. self.label_7.setText(QCoreApplication.translate("MainWindow", u"x", None))
  488. self.label_10.setText(QCoreApplication.translate("MainWindow", u"x", None))
  489. self.lineEdit_image_size_Z.setText(QCoreApplication.translate("MainWindow", u"Z", None))
  490. self.lineEdit_pixel_size_Z.setText(QCoreApplication.translate("MainWindow", u"Z", None))
  491. self.label_8.setText(QCoreApplication.translate("MainWindow", u"px", None))
  492. self.label_11.setText(QCoreApplication.translate("MainWindow", u"um", None))
  493. self.groupBox_visualizer.setTitle(QCoreApplication.translate("MainWindow", u"Visualizer", None))
  494. self.label_4.setText(QCoreApplication.translate("MainWindow", u"Channel:", None))
  495. self.label_12.setText(QCoreApplication.translate("MainWindow", u"Visualization Mode:", None))
  496. self.radioButton_plotZproject.setText(QCoreApplication.translate("MainWindow", u"Z project", None))
  497. self.radioButton_plotStack.setText(QCoreApplication.translate("MainWindow", u"Stack", None))
  498. self.groupBox_channels.setTitle(QCoreApplication.translate("MainWindow", u"Channels for quantification", None))
  499. self.label.setText(QCoreApplication.translate("MainWindow", u"Plasticity: ", None))
  500. self.comboBox_filter_type_chP.setItemText(0, QCoreApplication.translate("MainWindow", u"Select Filter", None))
  501. self.comboBox_filter_type_chP.setItemText(1, QCoreApplication.translate("MainWindow", u"Threshold", None))
  502. self.comboBox_filter_type_chP.setItemText(2, QCoreApplication.translate("MainWindow", u"Gaussian Blur", None))
  503. self.comboBox_filter_type_chP.setItemText(3, QCoreApplication.translate("MainWindow", u"Median Filter", None))
  504. self.comboBox_filter_type_chP.setItemText(4, QCoreApplication.translate("MainWindow", u"Rolling Ball", None))
  506. self.pushButton_applyfilter_chP.setText(QCoreApplication.translate("MainWindow", u"Apply", None))
  507. self.pushButton_undofilter_chP.setText(QCoreApplication.translate("MainWindow", u"Undo", None))
  508. self.label_3.setText(QCoreApplication.translate("MainWindow", u"Fluoresence:", None))
  509. self.comboBox_filter_type_chF.setItemText(0, QCoreApplication.translate("MainWindow", u"Select Filter", None))
  510. self.comboBox_filter_type_chF.setItemText(1, QCoreApplication.translate("MainWindow", u"Threshold", None))
  511. self.comboBox_filter_type_chF.setItemText(2, QCoreApplication.translate("MainWindow", u"Gaussian Blur", None))
  512. self.comboBox_filter_type_chF.setItemText(3, QCoreApplication.translate("MainWindow", u"Median Filter", None))
  513. self.comboBox_filter_type_chF.setItemText(4, QCoreApplication.translate("MainWindow", u"Rolling Ball", None))
  515. self.pushButton_applyfilter_chF.setText(QCoreApplication.translate("MainWindow", u"Apply", None))
  516. self.pushButton_undofilter_chF.setText(QCoreApplication.translate("MainWindow", u"Undo", None))
  517. self.groupBox_observations.setTitle(QCoreApplication.translate("MainWindow", u"Observation", None))
  518. self.groupBox_roi.setTitle(QCoreApplication.translate("MainWindow", u"Region of Interest (ROI) Selection", None))
  519. self.pushButton_roi.setText(QCoreApplication.translate("MainWindow", u"Create ROI", None))
  520. self.pushButton_apply_roi.setText(QCoreApplication.translate("MainWindow", u"Apply ROI", None))
  521. self.groupBox.setTitle(QCoreApplication.translate("MainWindow", u"Slice Selection", None))
  522. self.label_13.setText(QCoreApplication.translate("MainWindow", u"From:", None))
  523. self.label_14.setText(QCoreApplication.translate("MainWindow", u"To:", None))
  524. #if QT_CONFIG(tooltip)
  525. self.checkBox_show_distributions.setToolTip(QCoreApplication.translate("MainWindow", u"Display X, Y, Z distribution plots after processing", None))
  526. #endif // QT_CONFIG(tooltip)
  527. self.checkBox_show_distributions.setText(QCoreApplication.translate("MainWindow", u"Show distribution plots", None))
  528. self.pushButton_procces.setText(QCoreApplication.translate("MainWindow", u"Process image and save", None))
  529. # retranslateUi
  532. class MyMainWindow(QMainWindow):
  533. """
  534. Main application window for MorphoScope structural plasticity analysis.
  536. This class provides the graphical user interface and core functionality for:
  537. - Loading and visualizing 3D microscopy images
  538. - Applying preprocessing filters
  539. - Defining regions of interest (ROI)
  540. - Calculating structural plasticity metrics
  541. - Exporting results to CSV
  543. Attributes
  544. ----------
  545. ui : Ui_MainWindow
  546. Auto-generated UI from Qt Designer (PySide6)
  547. roi : pyqtgraph.PolyLineROI
  548. Current polygonal region of interest
  549. creating_roi : bool
  550. Flag indicating if ROI creation is active
  551. current_image_data : List[np.ndarray]
  552. Loaded image data (one array per channel)
  553. current_metadata_channel : List[str]
  554. Channel names/labels
  555. current_metadata_voxel_size : Tuple[float, float, float]
  556. Voxel dimensions (x, y, z) in micrometers
  557. current_metadata_dimension : Tuple[int, int, int]
  558. Image dimensions (width, height, depth)
  559. complexity_channel : np.ndarray
  560. Masked image for plasticity analysis
  561. fluor_channel : Optional[np.ndarray]
  562. Masked image for fluorescence analysis (if available)
  563. csv_file_path : str
  564. Path to output CSV file
  566. Notes
  567. -----
  568. - The UI must be generated from Qt Designer (.ui file) using pyside6-uic
  569. - Supports CZI, TIF, and LSM microscopy formats
  570. - Uses ImageProcessor for quantification (see image_processor.py)
  572. See Also
  573. --------
  574. image_processor.ImageProcessor : Core processing engine
  575. """
  577. def __init__(self):
  578. """
  579. Initialize the main window and connect UI elements to handlers.
  581. This method:
  582. 1. Sets up the auto-generated UI
  583. 2. Connects buttons to their respective functions
  584. 3. Initializes instance variables
  585. """
  586. super().__init__()
  587. self.ui = Ui_MainWindow()
  588. self.ui.setupUi(self)
  590. # ================================================================
  591. # CONNECT UI ELEMENTS TO HANDLERS
  592. # ================================================================
  594. # Image loading and management
  595. self.ui.pushButton_loadImage.clicked.connect(self.load_images)
  596. self.ui.pushButton_clean.clicked.connect(self.clean_list)
  597. self.ui.listWidget_images.itemSelectionChanged.connect(self.on_image_selected)
  599. # ROI selection
  600. self.ui.pushButton_roi.clicked.connect(self.enable_polygonal_roi_creation)
  601. self.ui.pushButton_apply_roi.clicked.connect(self.apply_roi_mask)
  603. # Image display controls
  604. self.ui.comboBox_channel_selector.currentIndexChanged.connect(self.update_display)
  605. self.ui.radioButton_plotZproject.toggled.connect(self.update_display)
  606. self.ui.radioButton_plotStack.toggled.connect(self.update_display)
  608. # Filter controls
  609. self.ui.pushButton_applyfilter_chP.clicked.connect(
  610. lambda: self.apply_selected_filter('chP')
  611. )
  612. self.ui.pushButton_applyfilter_chF.clicked.connect(
  613. lambda: self.apply_selected_filter('chF')
  614. )
  615. self.ui.pushButton_undofilter_chP.clicked.connect(
  616. lambda: self.undo_filter('chP')
  617. )
  618. self.ui.pushButton_undofilter_chF.clicked.connect(
  619. lambda: self.undo_filter('chF')
  620. )
  622. # Processing
  623. self.ui.pushButton_procces.clicked.connect(self.process)
  625. # ================================================================
  626. # INITIALIZE INSTANCE VARIABLES
  627. # ================================================================
  629. # ROI management
  630. self.roi = None
  631. self.creating_roi = False
  632. self.temp_points = []
  633. self.polygon_points = []
  634. self.AArea = 0.0
  636. # Image data
  637. self.current_image_filepath = None
  638. self.current_image_data = None
  639. self.original_image_data = None # Backup for undo filter
  640. self.current_metadata_channel = None
  641. self.current_metadata_dimension = None
  642. self.current_metadata_voxel_size = None
  644. # Processed channels
  645. self.complexity_channel = None
  646. self.fluor_channel = None
  648. # Output
  649. self.csv_file_path = None
  651. logger.info("MorphoScope main window initialized")
  654. # ====================================================================
  655. # IMAGE LOADING METHODS
  656. # ====================================================================
  658. def load_images(self):
  659. """
  660. Load microscopy images and set up CSV output file.
  662. This method:
  663. 1. Opens file dialog to select image files
  664. 2. Prompts for output CSV filename
  665. 3. Creates CSV with headers if new
  666. 4. Adds images to processing list
  668. Supported Formats
  669. -----------------
  670. - .czi : Zeiss CZI files
  671. - .tif : TIFF stacks
  672. - .lsm : Zeiss LSM files
  674. Notes
  675. -----
  676. - Duplicate files are automatically filtered out
  677. - CSV headers are written only for new files
  678. - All images share the same output CSV file
  679. """
  680. logger.info("Loading images...")
  682. # Open file selection dialog
  683. file_paths, _ = QFileDialog.getOpenFileNames(
  684. None,
  685. "Select Images",
  686. "",
  687. "Image Files (*.tif *.czi *.lsm)"
  688. )
  690. if not file_paths:
  691. QMessageBox.information(
  692. None,
  693. "No Files Selected",
  694. "Please select one or more image files."
  695. )
  696. return
  698. # Get output filename from user
  699. output_file_name, ok = QInputDialog.getText(
  700. None,
  701. "Output File Name",
  702. "Enter the name of the output CSV file:"
  703. )
  705. if not ok or not output_file_name.strip():
  706. QMessageBox.warning(
  707. None,
  708. "No Output File",
  709. "You must provide a name for the output file."
  710. )
  711. return
  713. # Ensure .csv extension
  714. if not output_file_name.endswith(".csv"):
  715. output_file_name += ".csv"
  717. # Determine output folder (same as first image)
  718. output_folder = os.path.dirname(file_paths[0]) if file_paths else os.getcwd()
  719. self.csv_file_path = os.path.join(output_folder, output_file_name)
  721. file_exists = os.path.isfile(self.csv_file_path)
  723. # Create CSV and write headers if new file
  724. try:
  725. with open(self.csv_file_path, mode='a', newline='', encoding='utf-8') as csv_file:
  726. writer = csv.writer(csv_file)
  727. if not file_exists:
  728. writer.writerow([
  729. "Image filename",
  730. "Spread x [pixel]",
  731. "Spread y [pixel]",
  732. "Spread z [pixel]",
  733. "Spread x*y [pixel2]",
  734. "Spread x*y*z [pixel3]",
  735. "Spread x [um]",
  736. "Spread y [um]",
  737. "Spread z [um]",
  738. "Spread x*y [um2]",
  739. "Spread x*y*z [um3]",
  740. "Axonal Volume",
  741. "Fluorescence_px",
  742. "Fluorescence_um",
  743. "Observation"
  744. ])
  745. logger.info(f"Created new CSV file: {self.csv_file_path}")
  746. except Exception as e:
  747. logger.error(f"Failed to create CSV file: {e}")
  748. QMessageBox.critical(
  749. self,
  750. "Error Creating File",
  751. f"An error occurred while creating the file:\n{e}"
  752. )
  753. return
  755. # Filter out duplicate files
  756. existing_files = [
  757. self.ui.listWidget_images.item(i).text()
  758. for i in range(self.ui.listWidget_images.count())
  759. ]
  760. new_files = [fp for fp in file_paths if fp not in existing_files]
  762. if not new_files:
  763. QMessageBox.information(
  764. self,
  765. "No New Files",
  766. "All selected files are already loaded."
  767. )
  768. return
  770. # Add new files to list
  771. self.ui.listWidget_images.addItems(new_files)
  773. logger.info(f"Loaded {len(new_files)} new images")
  774. QMessageBox.information(
  775. None,
  776. "Images Loaded",
  777. f"Loaded {len(new_files)} images. Ready to process."
  778. )
  781. def _load_czi(self, file_path: str):
  782. """
  783. Load a Zeiss CZI microscopy file.
  785. Parameters
  786. ----------
  787. file_path : str
  788. Path to .czi file
  790. Notes
  791. -----
  792. - Extracts metadata (voxel size, dimensions, channels)
  793. - Applies zero-padding for non-square images
  794. - Transposes data to (Z, X, Y) format
  796. Raises
  797. ------
  798. ValueError
  799. If required metadata keys are missing
  800. RuntimeError
  801. If file cannot be loaded
  802. """
  803. try:
  804. logger.info(f"Loading CZI file: {file_path}")
  806. with czi.open_czi(file_path) as czifile:
  807. # Extract metadata
  808. metadata = czifile.metadata
  810. width_px = int(metadata['ImageDocument']['Metadata']['Information']['Image']['SizeX'])
  811. height_px = int(metadata['ImageDocument']['Metadata']['Information']['Image']['SizeY'])
  812. zlim = int(metadata['ImageDocument']['Metadata']['Information']['Image']['SizeZ'])
  814. voxel_size = metadata['ImageDocument']['Metadata']['Scaling']['Items']['Distance']
  815. voxel_size_x_um = float(next(
  816. item for item in voxel_size if item['@Id'] == 'X'
  817. )['Value']) * 1e6
  818. voxel_size_y_um = float(next(
  819. item for item in voxel_size if item['@Id'] == 'Y'
  820. )['Value']) * 1e6
  821. voxel_size_z_um = float(next(
  822. item for item in voxel_size if item['@Id'] == 'Z'
  823. )['Value']) * 1e6
  825. num_channels = int(
  826. metadata['ImageDocument']['Metadata']['Information']['Image'].get('SizeC', 1)
  827. )
  828. channels = [f"Channel {i+1}" for i in range(num_channels)] if num_channels > 1 else ["Channel 1"]
  830. logger.debug(f"CZI metadata: {width_px}x{height_px}x{zlim}, "
  831. f"{num_channels} channels, voxel: {voxel_size_x_um:.3f}x"
  832. f"{voxel_size_y_um:.3f}x{voxel_size_z_um:.3f} µm")
  834. # Read data for each channel
  835. data = []
  836. for i in range(num_channels):
  837. channel_data = [
  838. czifile.read(plane={"C": i, "Z": z})[:, :, 0]
  839. for z in range(zlim)
  840. ]
  842. # Apply zero-padding for non-square images
  843. if width_px != height_px:
  844. max_dim = max(width_px, height_px)
  845. channel_data = np.array(channel_data)
  846. padded_image = np.zeros(
  847. (zlim, max_dim, max_dim),
  848. dtype=channel_data.dtype
  849. )
  850. y_start = (max_dim - height_px) // 2
  851. x_start = (max_dim - width_px) // 2
  852. padded_image[:, y_start:y_start+height_px, x_start:x_start+width_px] = channel_data
  853. channel_data = padded_image
  855. logger.debug(f"Applied zero-padding: {width_px}x{height_px} -> {max_dim}x{max_dim}")
  857. # Stack and transpose to (Z, X, Y)
  858. data.append(np.stack(channel_data, axis=0).transpose(0, 2, 1))
  860. # Update dimensions if padded
  861. if width_px != height_px:
  862. width_px = max_dim
  863. height_px = max_dim
  865. # Store loaded data
  866. self.current_image_data = data
  867. self.current_metadata_channel = channels
  868. self.current_metadata_voxel_size = (voxel_size_x_um, voxel_size_y_um, voxel_size_z_um)
  869. self.current_metadata_dimension = (width_px, height_px, zlim)
  871. logger.info(f"✓ CZI file loaded successfully")
  873. except KeyError as ke:
  874. logger.error(f"Metadata key not found: {ke}")
  875. raise ValueError(f"Metadata key not found: {ke}")
  876. except Exception as e:
  877. logger.error(f"Unexpected error loading CZI: {e}", exc_info=True)
  878. raise RuntimeError(f"Unexpected error while loading CZI file: {e}")
  881. def _load_tif(self, file_path: str):
  882. """
  883. Load a TIFF microscopy file.
  885. Parameters
  886. ----------
  887. file_path : str
  888. Path to .tif file
  890. Notes
  891. -----
  892. - Attempts to read ImageJ metadata for voxel sizes
  893. - Falls back to default values if metadata unavailable
  894. - Handles 2D, 3D, and 4D TIFF formats
  895. - Transposes data to (Z, X, Y) format
  897. Warnings
  898. --------
  899. If metadata is missing, default values are used:
  900. - voxel_size_x = 0.1 µm
  901. - voxel_size_y = 0.1 µm
  902. - voxel_size_z = 1.0 µm
  903. """
  904. try:
  905. logger.info(f"Loading TIF file: {file_path}")
  907. with tifffile.TiffFile(file_path) as tiff:
  908. # Try to read ImageJ metadata
  909. try:
  910. imagej_metadata = tiff.imagej_metadata
  911. if imagej_metadata is None:
  912. raise ValueError("Metadata is not available")
  914. num_channels = imagej_metadata.get('channels', 1)
  915. voxel_size_z = float(imagej_metadata.get('spacing', 1.0))
  917. logger.debug(f"ImageJ metadata: {num_channels} channels, z-spacing: {voxel_size_z} µm")
  919. except (AttributeError, ValueError):
  920. # Use default values if metadata unavailable
  921. logger.warning("No ImageJ metadata found. Using default values.")
  922. QMessageBox.warning(
  923. None,
  924. "Metadata Warning",
  925. "No metadata found. Using default values."
  926. )
  927. num_channels = 1
  928. voxel_size_z = 1.0
  930. # Assume isotropic XY voxels
  931. voxel_size_x = 0.1
  932. voxel_size_y = voxel_size_x
  934. # Read image data
  935. full_image = tiff.asarray()
  936. dims = full_image.ndim
  938. # Handle different dimensionalities
  939. if dims == 2:
  940. # Single slice, single channel
  941. image_data = full_image[np.newaxis, :, :]
  943. elif dims == 3:
  944. # Either (Z, Y, X) or (C, Y, X)
  945. if num_channels > 1 and full_image.shape[0] == num_channels:
  946. # Multi-channel, single Z
  947. image_data = [full_image[c, :, :][np.newaxis, :, :] for c in range(num_channels)]
  948. else:
  949. # Single channel, multiple Z
  950. image_data = full_image
  952. elif dims == 4:
  953. # Multi-channel, multiple Z: (Z, C, Y, X)
  954. image_data = [full_image[:, c, :, :] for c in range(num_channels)]
  956. else:
  957. raise ValueError(f"Unexpected image dimensions: {dims}")
  959. # Transpose to (Z, X, Y)
  960. if isinstance(image_data, list):
  961. image_data = [img.transpose(0, 2, 1) for img in image_data]
  962. else:
  963. image_data = image_data.transpose(0, 2, 1)
  965. # Get dimensions
  966. if num_channels == 1:
  967. height, width = image_data.shape[1:3]
  968. zlim = image_data.shape[0]
  969. data = [image_data]
  970. else:
  971. height, width = image_data[0].shape[1:3]
  972. zlim = image_data[0].shape[0]
  973. data = image_data
  975. # Store loaded data
  976. self.current_image_data = data
  977. self.current_metadata_channel = [f"Channel {i+1}" for i in range(num_channels)]
  978. self.current_metadata_voxel_size = (voxel_size_x, voxel_size_y, voxel_size_z)
  979. self.current_metadata_dimension = (width, height, zlim)
  981. logger.info(f"✓ TIF file loaded successfully: {width}x{height}x{zlim}")
  982. QMessageBox.information(
  983. None,
  984. "TIF Loaded",
  985. f"Successfully loaded {file_path}."
  986. )
  988. except Exception as e:
  989. logger.error(f"Failed to load TIF: {e}", exc_info=True)
  990. QMessageBox.critical(
  991. None,
  992. "Error Loading TIF",
  993. f"Failed to load TIF file:\n{e}"
  994. )
  997. def _load_lsm(self, file_path: str):
  998. """
  999. Load a Zeiss LSM microscopy file.
  1001. Parameters
  1002. ----------
  1003. file_path : str
  1004. Path to .lsm file
  1006. Notes
  1007. -----
  1008. - LSM files are a special type of TIFF with Zeiss metadata
  1009. - Extracts voxel sizes from LSM metadata
  1010. - Transposes data to (Z, X, Y) format
  1011. """
  1012. try:
  1013. logger.info(f"Loading LSM file: {file_path}")
  1015. with tifffile.TiffFile(file_path) as tif:
  1016. # Extract LSM metadata
  1017. metadata = tif.lsm_metadata
  1019. num_channels = metadata['DimensionChannels']
  1020. zlim = metadata['DimensionZ']
  1021. width = metadata['DimensionX']
  1022. height = metadata['DimensionY']
  1024. # Convert voxel sizes to micrometers
  1025. voxel_size_x = metadata['VoxelSizeX'] * 1e6
  1026. voxel_size_y = metadata['VoxelSizeY'] * 1e6
  1027. voxel_size_z = metadata['VoxelSizeZ'] * 1e6
  1029. logger.debug(f"LSM metadata: {width}x{height}x{zlim}, {num_channels} channels, "
  1030. f"voxel: {voxel_size_x:.3f}x{voxel_size_y:.3f}x{voxel_size_z:.3f} µm")
  1032. # Read image data
  1033. if num_channels == 1:
  1034. # Single channel
  1035. image_data = tif.asarray().transpose((0, 2, 1)) # (Z, X, Y)
  1036. else:
  1037. # Multi-channel: (Z, C, Y, X)
  1038. full_image = tif.asarray(series=0)
  1039. image_data = [
  1040. full_image[:, c, :, :].transpose((0, 2, 1))
  1041. for c in range(num_channels)
  1042. ]
  1044. # Store loaded data
  1045. self.current_image_data = image_data if num_channels > 1 else [image_data]
  1046. self.current_metadata_channel = [f"Channel {i+1}" for i in range(num_channels)]
  1047. self.current_metadata_voxel_size = (voxel_size_x, voxel_size_y, voxel_size_z)
  1048. self.current_metadata_dimension = (width, height, zlim)
  1050. logger.info(f"✓ LSM file loaded successfully")
  1051. QMessageBox.information(
  1052. None,
  1053. "LSM Loaded",
  1054. f"Successfully loaded {file_path}."
  1055. )
  1057. except Exception as e:
  1058. logger.error(f"Failed to load LSM: {e}", exc_info=True)
  1059. QMessageBox.critical(
  1060. None,
  1061. "Error Loading LSM",
  1062. f"Failed to load LSM file:\n{e}"
  1063. )
  1066. # ====================================================================
  1067. # UI MANAGEMENT METHODS
  1068. # ====================================================================
  1070. def clean_list(self):
  1071. """
  1072. Clear all loaded images and reset the application state.
  1074. This method:
  1075. - Clears the image list widget
  1076. - Resets all image data variables
  1077. - Removes any active ROI
  1078. - Clears the display
  1079. - Re-enables channel selectors
  1080. """
  1081. logger.info("Cleaning image list and resetting state")
  1083. # Clear image list
  1084. self.ui.listWidget_images.clear()
  1086. # Reset data
  1087. self.current_image_data = None
  1088. self.original_image_data = None
  1089. self.current_metadata_channel = None
  1090. self.current_metadata_dimension = None
  1091. self.current_metadata_voxel_size = None
  1093. # Re-enable channel selectors
  1094. self.ui.comboBox_plasticityChannel.setEnabled(True)
  1095. self.ui.comboBox_fluoChannel.setEnabled(True)
  1097. # Clear display
  1098. self.ui.graphWidget.clear()
  1100. # Cancel ROI creation if active
  1101. if self.creating_roi:
  1102. self.creating_roi = False
  1103. self.temp_points = []
  1104. if hasattr(self, "vertex_scatter"):
  1105. self.ui.graphWidget.removeItem(self.vertex_scatter)
  1106. self.vertex_scatter = None
  1107. self.ui.pushButton_roi.setEnabled(True)
  1108. self.ui.pushButton_roi.setStyleSheet("")
  1110. # Remove existing ROI
  1111. self.clear_polygonal_roi()
  1112. if self.roi is not None:
  1113. self.ui.graphWidget.removeItem(self.roi)
  1114. self.roi = None
  1116. logger.info("✓ Application state reset")
  1119. def reset_image_data(self):
  1120. """
  1121. Reset current image data variables.
  1123. Used when switching between images in the list.
  1124. """
  1125. self.current_image_filepath = None
  1126. self.current_image_data = None
  1127. self.original_image_data = None
  1128. self.current_metadata_channel = None
  1129. self.current_metadata_dimension = None
  1130. self.current_metadata_voxel_size = None
  1131. self.ui.graphWidget.clear()
  1134. def on_image_selected(self):
  1135. """
  1136. Handle image selection from the list widget.
  1138. This method:
  1139. 1. Resets previous image data
  1140. 2. Loads the selected image file
  1141. 3. Updates channel selectors
  1142. 4. Displays image metadata
  1143. 5. Shows initial visualization
  1145. Notes
  1146. -----
  1147. - Maintains channel selection when switching between images of same format
  1148. - Automatically detects file format and calls appropriate loader
  1149. - Updates UI with image dimensions and voxel sizes
  1150. """
  1151. logger.info("Image selected from list")
  1153. self.reset_image_data()
  1155. # Get selected file
  1156. selected_items = self.ui.listWidget_images.selectedItems()
  1157. if not selected_items:
  1158. return
  1160. selected_file = selected_items[0].text()
  1161. self.current_image_filepath = selected_file
  1163. logger.info(f"Loading: {os.path.basename(selected_file)}")
  1165. # Clear display and ROI
  1166. self.ui.graphWidget.clear()
  1168. # Cancel ROI creation if active
  1169. if self.creating_roi:
  1170. self.creating_roi = False
  1171. self.temp_points = []
  1172. if hasattr(self, "vertex_scatter"):
  1173. self.ui.graphWidget.removeItem(self.vertex_scatter)
  1174. self.vertex_scatter = None
  1175. self.ui.pushButton_roi.setEnabled(True)
  1176. self.ui.pushButton_roi.setStyleSheet("")
  1178. self.clear_polygonal_roi()
  1179. if self.roi is not None:
  1180. self.ui.graphWidget.removeItem(self.roi)
  1181. self.roi = None
  1183. # Load image based on file extension
  1184. try:
  1185. if selected_file.endswith(".czi"):
  1186. self._load_czi(selected_file)
  1187. elif selected_file.endswith(".tif"):
  1188. self._load_tif(selected_file)
  1189. elif selected_file.endswith(".lsm"):
  1190. self._load_lsm(selected_file)
  1191. else:
  1192. QMessageBox.warning(
  1193. None,
  1194. "Unsupported Format",
  1195. f"Unsupported file format: {selected_file}"
  1196. )
  1197. return
  1198. except Exception as e:
  1199. logger.error(f"Failed to load image: {e}", exc_info=True)
  1200. QMessageBox.critical(
  1201. None,
  1202. "Error Loading Image",
  1203. f"Error loading image:\n{e}"
  1204. )
  1205. return
  1207. # Save previous channel selections
  1208. prev_index_plasticity = self.ui.comboBox_plasticityChannel.currentIndex()
  1209. prev_index_fluo = self.ui.comboBox_fluoChannel.currentIndex()
  1210. prev_channel_count = self.ui.comboBox_plasticityChannel.count()
  1212. # Update channel selectors
  1213. self.ui.comboBox_plasticityChannel.setEnabled(True)
  1214. self.ui.comboBox_fluoChannel.setEnabled(True)
  1216. self.ui.comboBox_channel_selector.clear()
  1217. self.ui.comboBox_channel_selector.addItems(self.current_metadata_channel)
  1219. self.ui.comboBox_plasticityChannel.clear()
  1220. self.ui.comboBox_plasticityChannel.addItems(self.current_metadata_channel)
  1222. self.ui.comboBox_fluoChannel.clear()
  1223. self.ui.comboBox_fluoChannel.addItem("No channel")
  1224. self.ui.comboBox_fluoChannel.addItems(self.current_metadata_channel)
  1226. # Restore previous selection if possible
  1227. new_channel_count = len(self.current_metadata_channel)
  1228. if prev_channel_count == new_channel_count:
  1229. if 0 <= prev_index_plasticity < self.ui.comboBox_plasticityChannel.count():
  1230. self.ui.comboBox_plasticityChannel.setCurrentIndex(prev_index_plasticity)
  1231. if 0 <= prev_index_fluo + 1 < self.ui.comboBox_fluoChannel.count():
  1232. self.ui.comboBox_fluoChannel.setCurrentIndex(prev_index_fluo)
  1233. else:
  1234. # Default selection for different channel count
  1235. self.ui.comboBox_plasticityChannel.setCurrentIndex(0)
  1236. self.ui.comboBox_fluoChannel.setCurrentIndex(0)
  1238. # Update metadata display
  1239. image_size_x, image_size_y, image_size_z = self.current_metadata_dimension
  1240. voxel_size_x, voxel_size_y, voxel_size_z = self.current_metadata_voxel_size
  1242. self.ui.lineEdit_image_size_X.setText(str(image_size_x))
  1243. self.ui.lineEdit_image_size_Y.setText(str(image_size_y))
  1244. self.ui.lineEdit_image_size_Z.setText(str(image_size_z))
  1245. self.ui.lineEdit_pixel_size_X.setText(f"{voxel_size_x:.3f}")
  1246. self.ui.lineEdit_pixel_size_Y.setText(f"{voxel_size_y:.3f}")
  1247. self.ui.lineEdit_pixel_size_Z.setText(f"{voxel_size_z:.3f}")
  1249. self.ui.spinBox_zmax.setValue(image_size_z - 1)
  1251. # Display image
  1252. if self.ui.radioButton_plotZproject.isChecked():
  1253. # Show maximum Z projection
  1254. max_projection = np.max(self.current_image_data[0], axis=0)
  1255. self.ui.graphWidget.setImage(max_projection)
  1256. elif self.ui.radioButton_plotStack.isChecked():
  1257. # Show full stack
  1258. self.ui.graphWidget.setImage(self.current_image_data[0])
  1259. else:
  1260. QMessageBox.warning(
  1261. self,
  1262. "Display Mode",
  1263. "Please select either Z-projection or Stack view."
  1264. )
  1266. # Hide ROI button (not needed for this application)
  1267. self.ui.graphWidget.ui.roiBtn.hide()
  1269. logger.info(f"✓ Image loaded and displayed: {image_size_x}x{image_size_y}x{image_size_z}")
  1272. def update_display(self):
  1273. """
  1274. Update the image display based on current channel and view mode selection.
  1276. Called automatically when:
  1277. - Channel selector changes
  1278. - View mode radio button toggles (Z-projection vs Stack)
  1280. View Modes
  1281. ----------
  1282. - Z-projection: Maximum intensity projection along Z axis
  1283. - Stack: Full 3D stack (can scroll through slices)
  1284. """
  1285. # Check if image is loaded
  1286. selected_items = self.ui.listWidget_images.selectedItems()
  1287. if not selected_items:
  1288. return
  1290. selected_channel = self.ui.comboBox_channel_selector.currentIndex()
  1292. if 0 <= selected_channel < len(self.current_image_data):
  1293. channel_data = self.current_image_data[selected_channel]
  1295. if self.ui.radioButton_plotZproject.isChecked():
  1296. # Show maximum Z projection
  1297. max_projection = np.max(channel_data, axis=0)
  1298. self.ui.graphWidget.setImage(max_projection)
  1299. logger.debug(f"Displaying Z-projection of channel {selected_channel}")
  1301. elif self.ui.radioButton_plotStack.isChecked():
  1302. # Show full stack
  1303. self.ui.graphWidget.setImage(channel_data)
  1304. logger.debug(f"Displaying full stack of channel {selected_channel}")
  1306. else:
  1307. QMessageBox.warning(
  1308. self,
  1309. "Display Mode",
  1310. "Please select either Z-projection or Stack view."
  1311. )
  1314. # ====================================================================
  1315. # IMAGE FILTERING METHODS
  1316. # ====================================================================
  1318. def apply_selected_filter(self, channel: str):
  1319. """
  1320. Apply the selected filter to the specified channel.
  1322. Parameters
  1323. ----------
  1324. channel : str
  1325. Channel identifier: 'chP' (plasticity) or 'chF' (fluorescence)
  1327. Available Filters
  1328. -----------------
  1329. - Threshold: Remove pixels below percentage of maximum intensity
  1330. - Gaussian Blur: Smooth image with Gaussian kernel
  1331. - Median Filter: Remove noise with median filter
  1333. Notes
  1334. -----
  1335. - Original image is backed up before filtering (for undo)
  1336. - User is prompted for filter parameters via dialog
  1337. - Display is automatically updated after filtering
  1338. """
  1339. logger.info(f"Applying filter to channel: {channel}")
  1341. # Get channel index and filter type
  1342. if channel == 'chP':
  1343. selected_filter = self.ui.comboBox_filter_type_chP.currentText()
  1344. channel_index = self.ui.comboBox_plasticityChannel.currentIndex()
  1345. elif channel == 'chF':
  1346. selected_filter = self.ui.comboBox_filter_type_chF.currentText()
  1347. channel_index = self.ui.comboBox_fluoChannel.currentIndex() - 1
  1348. else:
  1349. QMessageBox.warning(self, "Invalid Channel", "Invalid channel specified.")
  1350. return
  1352. # Validate channel index
  1353. if not (0 <= channel_index < len(self.current_image_data)):
  1354. QMessageBox.warning(
  1355. self,
  1356. "Invalid Channel",
  1357. f"Invalid channel index: {channel_index}"
  1358. )
  1359. return
  1361. # Backup original image (for undo)
  1362. if self.original_image_data is None:
  1363. self.original_image_data = {}
  1364. if channel_index not in self.original_image_data:
  1365. self.original_image_data[channel_index] = self.current_image_data[channel_index].copy()
  1366. logger.debug(f"Backed up original image for channel {channel_index}")
  1368. # Get image copy
  1369. image = self.current_image_data[channel_index].copy()
  1371. # Apply selected filter
  1372. if selected_filter == "Threshold":
  1373. threshold, ok = QInputDialog.getDouble(
  1374. self,
  1375. "Threshold",
  1376. "Percentage of maximum (0-100):",
  1377. 3.0, 0, 100, 1
  1378. )
  1379. if ok:
  1380. max_val = np.max(image)
  1381. image[image <= (threshold / 100.0) * max_val] = 0
  1382. logger.info(f"Applied threshold: {threshold}% of max ({max_val:.2f})")
  1384. elif selected_filter == "Gaussian Blur":
  1385. sigma, ok = QInputDialog.getDouble(
  1386. self,
  1387. "Gaussian Blur",
  1388. "Sigma:",
  1389. 1.0, 0.1, 50.0, 1
  1390. )
  1391. if ok:
  1392. image = gaussian(image, sigma=sigma, preserve_range=True)
  1393. logger.info(f"Applied Gaussian blur: sigma={sigma}")
  1395. elif selected_filter == "Median Filter":
  1396. size, ok = QInputDialog.getInt(
  1397. self,
  1398. "Median Filter",
  1399. "Kernel size (odd):",
  1400. 3, 1, 99, 2
  1401. )
  1402. if ok:
  1403. filtered_slices = [
  1404. median_filter(image[z], size=size)
  1405. for z in range(image.shape[0])
  1406. ]
  1407. image = np.stack(filtered_slices, axis=0)
  1408. logger.info(f"Applied median filter: size={size}")
  1410. else:
  1411. QMessageBox.warning(self, "Invalid Filter", "Please select a valid filter.")
  1412. return
  1414. # Save filtered image and update display
  1415. self.current_image_data[channel_index] = image
  1416. self.update_display()
  1418. logger.info(f"✓ Filter applied successfully to channel {channel_index}")
  1421. def undo_filter(self, channel: str):
  1422. """
  1423. Undo the last filter applied to the specified channel.
  1425. Parameters
  1426. ----------
  1427. channel : str
  1428. Channel identifier: 'chP' (plasticity) or 'chF' (fluorescence)
  1430. Notes
  1431. -----
  1432. - Restores the original image from backup
  1433. - Removes backup after restoring
  1434. - Only one undo level is supported
  1435. """
  1436. logger.info(f"Undoing filter for channel: {channel}")
  1438. # Get channel index
  1439. if channel == 'chP':
  1440. channel_index = self.ui.comboBox_plasticityChannel.currentIndex()
  1441. elif channel == 'chF':
  1442. channel_index = self.ui.comboBox_fluoChannel.currentIndex() - 1
  1443. else:
  1444. QMessageBox.warning(self, "Invalid Channel", "Invalid channel specified.")
  1445. return
  1447. # Check if backup exists
  1448. if self.original_image_data is None or channel_index not in self.original_image_data:
  1449. QMessageBox.information(
  1450. self,
  1451. "No Backup",
  1452. "No original version saved for this channel."
  1453. )
  1454. return
  1456. # Restore original image
  1457. self.current_image_data[channel_index] = self.original_image_data[channel_index].copy()
  1458. del self.original_image_data[channel_index]
  1460. # Clean up backup dict if empty
  1461. if not self.original_image_data:
  1462. self.original_image_data = None
  1464. self.update_display()
  1466. logger.info(f"✓ Filter undone for channel {channel_index}")
  1469. # ====================================================================
  1470. # ROI SELECTION METHODS
  1471. # ====================================================================
  1473. def enable_polygonal_roi_creation(self):
  1474. """
  1475. Enable interactive polygonal ROI creation mode.
  1477. In this mode:
  1478. - Click to add vertices to polygon
  1479. - Backspace/Delete/Space to remove last vertex
  1480. - Escape to cancel ROI creation
  1481. - Apply ROI button to finalize selection
  1483. Notes
  1484. -----
  1485. - Vertices are displayed as red dots
  1486. - Button turns green while in ROI creation mode
  1487. - Mouse and keyboard events are captured
  1488. """
  1489. logger.info("Enabling polygonal ROI creation")
  1491. self.creating_roi = True
  1492. self.temp_points = []
  1494. # Create scatter plot for vertices
  1495. self.vertex_scatter = pyqtgraph.ScatterPlotItem(
  1496. size=5,
  1497. pen=pyqtgraph.mkPen(None),
  1498. brush=pyqtgraph.mkBrush(255, 0, 0, 150)
  1499. )
  1500. self.ui.graphWidget.addItem(self.vertex_scatter)
  1502. # Connect mouse click event
  1503. self.ui.graphWidget.view.scene().sigMouseClicked.connect(self.add_vertex)
  1505. # Override keyboard event handler
  1506. self.ui.graphWidget.keyPressEvent = self.handle_key_press
  1508. # Update button appearance
  1509. self.ui.pushButton_roi.setStyleSheet("background-color: lightgreen;")
  1510. self.ui.pushButton_roi.setEnabled(False)
  1512. logger.info("✓ ROI creation mode active")
  1515. def add_vertex(self, event):
  1516. """
  1517. Add a vertex to the polygon ROI on mouse click.
  1519. Parameters
  1520. ----------
  1521. event : QGraphicsSceneMouseEvent
  1522. Mouse click event
  1524. Notes
  1525. -----
  1526. - Only active when creating_roi flag is True
  1527. - Converts scene coordinates to image coordinates
  1528. - Updates vertex visualization immediately
  1529. """
  1530. # Check if ROI creation is enabled
  1531. if not getattr(self, 'creating_roi', False):
  1532. return
  1534. # Get click position in image coordinates
  1535. pos = event.scenePos()
  1536. img_pos = self.ui.graphWidget.view.mapSceneToView(pos)
  1537. self.temp_points.append((img_pos.x(), img_pos.y()))
  1539. # Update vertex visualization
  1540. self.vertex_scatter.setData(
  1541. [p[0] for p in self.temp_points],
  1542. [p[1] for p in self.temp_points]
  1543. )
  1545. logger.debug(f"Added vertex: ({img_pos.x():.1f}, {img_pos.y():.1f})")
  1548. def handle_key_press(self, event):
  1549. """
  1550. Handle keyboard events during ROI creation.
  1552. Parameters
  1553. ----------
  1554. event : QKeyEvent
  1555. Keyboard event
  1557. Key Bindings
  1558. ------------
  1559. - Backspace/Delete/Space/Left: Remove last vertex
  1560. - Escape: Cancel ROI creation
  1561. """
  1562. key = event.key()
  1564. # Remove last vertex
  1565. if key in [Qt.Key_Backspace, Qt.Key_Delete,
  1566. Qt.Key_Space, Qt.Key_Left]:
  1567. if self.temp_points:
  1568. removed_point = self.temp_points.pop()
  1569. logger.debug(f"Removed vertex: {removed_point}")
  1571. # Update visualization
  1572. self.vertex_scatter.setData(
  1573. [p[0] for p in self.temp_points],
  1574. [p[1] for p in self.temp_points]
  1575. )
  1576. else:
  1577. logger.debug("No vertices to remove")
  1579. # Cancel ROI creation
  1580. elif key == Qt.Key_Escape:
  1581. logger.info("ROI creation canceled")
  1582. self.creating_roi = False
  1583. self.temp_points = []
  1585. if hasattr(self, "vertex_scatter"):
  1586. self.ui.graphWidget.removeItem(self.vertex_scatter)
  1587. self.vertex_scatter = None
  1589. # Restore button
  1590. self.ui.pushButton_roi.setEnabled(True)
  1591. self.ui.pushButton_roi.setStyleSheet("")
  1594. def clear_polygonal_roi(self):
  1595. """
  1596. Clear all temporary ROI data.
  1598. Removes:
  1599. - Vertex scatter plot
  1600. - Temporary point list
  1601. """
  1602. if hasattr(self, 'vertex_scatter') and self.vertex_scatter is not None:
  1603. self.ui.graphWidget.removeItem(self.vertex_scatter)
  1604. self.vertex_scatter = None
  1605. self.temp_points = []
  1608. def apply_roi_mask(self):
  1609. """
  1610. Apply the defined ROI mask to the selected channels.
  1612. This method:
  1613. 1. Finalizes the polygon ROI
  1614. 2. Calculates ROI area
  1615. 3. Creates binary mask
  1616. 4. Applies mask to plasticity channel
  1617. 5. Applies mask to fluorescence channel (if selected)
  1618. 6. Updates display
  1619. 7. Disables channel selectors (locked for processing)
  1621. Notes
  1622. -----
  1623. - Minimum 3 vertices required for valid polygon
  1624. - Mask is 2D, replicated across all Z slices
  1625. - Masked regions are set to zero
  1626. - Original images remain unchanged (copies are masked)
  1628. Raises
  1629. ------
  1630. Warning
  1631. If no ROI defined or less than 3 vertices
  1632. """
  1633. logger.info("Applying ROI mask...")
  1635. # Validate ROI
  1636. if self.roi is None:
  1637. if not hasattr(self, 'temp_points') or len(self.temp_points) < 3:
  1638. QMessageBox.warning(
  1639. self,
  1640. "No ROI",
  1641. "Please select an ROI or create one with at least 3 vertices."
  1642. )
  1643. return
  1645. # Close polygon automatically
  1646. self.temp_points.append(self.temp_points[0])
  1647. self.roi = pyqtgraph.PolyLineROI(
  1648. self.temp_points,
  1649. closed=True,
  1650. pen=pyqtgraph.mkPen('g', width=2)
  1651. )
  1652. self.ui.graphWidget.addItem(self.roi)
  1654. # Deactivate ROI creation mode
  1655. self.creating_roi = False
  1656. self.ui.pushButton_roi.setEnabled(True)
  1657. self.ui.pushButton_roi.setStyleSheet("")
  1659. # Get ROI vertices
  1660. roi_positions = self.roi.getLocalHandlePositions()
  1661. vertices = [(pos.x(), pos.y()) for name, pos in roi_positions]
  1663. # Calculate area and store vertices
  1664. polygon = np.array(vertices + [vertices[0]]) # Close polygon
  1665. self.AArea = Polygon(polygon).area
  1666. self.polygon_points = vertices
  1668. logger.info(f"ROI area: {self.AArea:.2f} pixels²")
  1670. # Get selected channels
  1671. plasticity_channel_index = self.ui.comboBox_plasticityChannel.currentIndex()
  1672. self.ui.comboBox_plasticityChannel.setEnabled(False) # Lock selection
  1674. fluo_channel_index = self.ui.comboBox_fluoChannel.currentIndex()
  1675. self.ui.comboBox_fluoChannel.setEnabled(False) # Lock selection
  1677. # Validate plasticity channel
  1678. if 0 <= plasticity_channel_index < len(self.current_image_data):
  1679. plasticity_image = self.current_image_data[plasticity_channel_index]
  1680. else:
  1681. QMessageBox.warning(
  1682. self,
  1683. "Invalid Channel",
  1684. "Invalid plasticity channel selected."
  1685. )
  1686. return
  1688. # Create binary mask from ROI
  1689. slices, height, width = plasticity_image.shape
  1691. # Create coordinate grid
  1692. y, x = np.meshgrid(np.arange(width), np.arange(height), indexing='xy')
  1693. points = np.vstack((x.ravel(), y.ravel())).T
  1695. # Check which points are inside polygon
  1696. path = MPLPath(polygon)
  1697. mask = path.contains_points(points).reshape(height, width)
  1699. # Expand mask to 3D (replicate for all Z slices)
  1700. expanded_mask = np.stack([mask] * slices, axis=0)
  1702. logger.info(f"ROI mask created: {np.sum(mask)} pixels, "
  1703. f"{slices} slices = {np.sum(expanded_mask)} total voxels")
  1705. # Apply mask to plasticity channel
  1706. masked_plasticity_image = np.copy(plasticity_image)
  1707. masked_plasticity_image[~expanded_mask] = 0
  1708. self.complexity_channel = masked_plasticity_image
  1710. # Update display
  1711. self.ui.graphWidget.setImage(masked_plasticity_image, autoLevels=True)
  1713. # Apply mask to fluorescence channel (if selected)
  1714. if fluo_channel_index == 0:
  1715. # "No channel" selected
  1716. fluo_image = None
  1717. elif 0 < fluo_channel_index <= len(self.current_image_data):
  1718. fluo_image = self.current_image_data[fluo_channel_index - 1]
  1719. else:
  1720. QMessageBox.warning(
  1721. self,
  1722. "Invalid Channel",
  1723. "Invalid fluorescence channel selected."
  1724. )
  1725. return
  1727. if fluo_image is not None:
  1728. masked_fluo_image = np.copy(fluo_image)
  1729. masked_fluo_image[~expanded_mask] = 0
  1730. self.fluor_channel = masked_fluo_image
  1731. logger.info("Fluorescence channel masked")
  1732. else:
  1733. self.fluor_channel = None
  1734. logger.info("No fluorescence channel selected")
  1736. logger.info(f"✓ ROI mask applied - Complexity channel: "
  1737. f"{np.count_nonzero(self.complexity_channel)} non-zero voxels, "
  1738. f"intensity: {np.sum(self.complexity_channel):.2f}")
  1741. # ====================================================================
  1742. # PROCESSING METHODS
  1743. # ====================================================================
  1745. def process(self):
  1746. """
  1747. Process the selected image to calculate structural plasticity metrics.
  1749. This is the main processing pipeline that:
  1750. 1. Validates parameters and ROI
  1751. 2. Extracts Z-range subset
  1752. 3. Applies ROI mask
  1753. 4. Initializes ImageProcessor
  1754. 5. Calculates PCA rotation and spreads
  1755. 6. Calculates fluorescence (if second channel)
  1756. 7. Plots distributions (optional)
  1757. 8. Saves results to CSV
  1758. 9. Updates UI
  1760. Workflow Steps
  1761. --------------
  1762. 1. Parameter validation
  1763. 2. Progress dialog creation
  1764. 3. Image preparation (ROI masking, Z-subset)
  1765. 4. Processor initialization
  1766. 5. PCA and spread calculation
  1767. 6. Fluorescence calculation (optional)
  1768. 7. Distribution plotting (optional)
  1769. 8. Results export to CSV
  1770. 9. UI update and success message
  1772. Notes
  1773. -----
  1774. - Shows progress dialog during processing
  1775. - Can be canceled by user at any time
  1776. - Errors are logged and displayed to user
  1777. - Processed images are marked in the list (green=success, red=error)
  1779. See Also
  1780. --------
  1781. ImageProcessor.process_image : Core processing algorithm
  1782. _validate_processing_parameters : Parameter validation
  1783. _prepare_masked_images : Image preparation
  1784. _save_results_to_csv : Results export
  1785. """
  1786. try:
  1787. logger.info("\n" + "="*70)
  1788. logger.info("STARTING PROCESSING")
  1789. logger.info("="*70)
  1791. # ============================================================
  1792. # STEP 1: VALIDATE PARAMETERS
  1793. # ============================================================
  1794. if not self._validate_processing_parameters():
  1795. return
  1797. # ============================================================
  1798. # STEP 2: GET PARAMETERS
  1799. # ============================================================
  1800. try:
  1801. voxel_size_x = float(self.ui.lineEdit_pixel_size_X.text())
  1802. voxel_size_y = float(self.ui.lineEdit_pixel_size_Y.text())
  1803. voxel_size_z = float(self.ui.lineEdit_pixel_size_Z.text())
  1804. z_start = self.ui.spinBox_zmin.value()
  1805. z_end = self.ui.spinBox_zmax.value()
  1806. except ValueError as e:
  1807. QMessageBox.critical(
  1808. self,
  1809. "Invalid Parameters",
  1810. f"Please check your numeric inputs:\n{str(e)}"
  1811. )
  1812. return
  1814. logger.info(f"Parameters: voxel_x={voxel_size_x:.3f}µm, "
  1815. f"voxel_y={voxel_size_y:.3f}µm, voxel_z={voxel_size_z:.3f}µm, "
  1816. f"z_range=[{z_start}, {z_end}]")
  1818. # Validate voxel sizes
  1819. is_valid, error_msg = validate_parameters(
  1820. voxel_size_x, voxel_size_y, voxel_size_z
  1821. )
  1822. if not is_valid:
  1823. QMessageBox.warning(self, "Invalid Voxel Sizes", error_msg)
  1824. return
  1826. # ============================================================
  1827. # STEP 3: CREATE PROGRESS DIALOG
  1828. # ============================================================
  1829. progress = QProgressDialog(
  1830. "Processing image...",
  1831. "Cancel",
  1832. 0, 100,
  1833. self
  1834. )
  1835. progress.setWindowModality(Qt.WindowModal)
  1836. progress.setWindowTitle("Structural Plasticity Analysis")
  1837. progress.setMinimumDuration(0) # Show immediately
  1838. progress.setValue(5)
  1840. # ============================================================
  1841. # STEP 4: PREPARE MASKED IMAGES
  1842. # ============================================================
  1843. progress.setLabelText("Applying ROI mask...")
  1844. progress.setValue(15)
  1846. masked_image_complexity, masked_image_fluor = self._prepare_masked_images(
  1847. z_start, z_end
  1848. )
  1850. if masked_image_complexity is None:
  1851. progress.close()
  1852. return
  1854. if progress.wasCanceled():
  1855. logger.info("Processing canceled by user")
  1856. progress.close()
  1857. return
  1859. progress.setValue(30)
  1861. # ============================================================
  1862. # STEP 5: INITIALIZE PROCESSOR
  1863. # ============================================================
  1864. progress.setLabelText("Initializing processor...")
  1866. processor = ImageProcessor(
  1867. voxel_size_x=voxel_size_x,
  1868. voxel_size_y=voxel_size_y,
  1869. voxel_size_z=voxel_size_z
  1870. )
  1872. progress.setValue(40)
  1874. # ============================================================
  1875. # STEP 6: PROCESS IMAGE (PCA + SPREADS)
  1876. # ============================================================
  1877. progress.setLabelText("Calculating PCA and spreads...")
  1879. logger.info(f"Processing complexity channel. Shape: {masked_image_complexity.shape}")
  1881. results = processor.process_image(
  1882. image_3d=masked_image_complexity,
  1883. mask_area_pixels=self.AArea
  1884. )
  1886. if progress.wasCanceled():
  1887. logger.info("Processing canceled by user")
  1888. progress.close()
  1889. return
  1891. progress.setValue(70)
  1893. # ============================================================
  1894. # STEP 7: CALCULATE FLUORESCENCE (if second channel exists)
  1895. # ============================================================
  1896. if masked_image_fluor is not None:
  1897. progress.setLabelText("Calculating fluorescence...")
  1898. logger.info("Calculating fluorescence for second channel")
  1900. fluor_px, fluor_um = processor.calculate_fluorescence(
  1901. masked_image_fluor,
  1902. self.AArea
  1903. )
  1905. results['fluorescence_px'] = fluor_px
  1906. results['fluorescence_um'] = fluor_um
  1908. progress.setValue(80)
  1910. # ============================================================
  1911. # STEP 8: PLOT DISTRIBUTIONS (if enabled)
  1912. # ============================================================
  1913. if self.ui.checkBox_show_distributions.isChecked():
  1914. self._plot_distributions(
  1915. results['MMsum'],
  1916. results['MMyy'],
  1917. results['MMzz']
  1918. )
  1920. # ============================================================
  1921. # STEP 9: SAVE RESULTS
  1922. # ============================================================
  1923. progress.setLabelText("Saving results...")
  1924. progress.setValue(90)
  1926. self._save_results_to_csv(results)
  1928. # ============================================================
  1929. # STEP 10: UPDATE UI
  1930. # ============================================================
  1931. self._update_ui_after_processing(success=True)
  1933. progress.setValue(100)
  1934. progress.close()
  1936. # ============================================================
  1937. # STEP 11: SHOW SUCCESS MESSAGE
  1938. # ============================================================
  1939. QMessageBox.information(
  1940. self,
  1941. "Processing Complete",
  1942. f"Image processed successfully!\n\n"
  1943. f"3D Spread: {results['spread_xyz_um']:.2f} µm³\n"
  1944. f"Axonal Volume: {results['axonal_volume']:.2f}\n"
  1945. f"Rotation Angle: {results['rotation_angle']:.2f}°"
  1946. )
  1948. logger.info("="*70)
  1949. logger.info("PROCESSING COMPLETED SUCCESSFULLY")
  1950. logger.info("="*70 + "\n")
  1952. except Exception as e:
  1953. logger.error(f"Processing error: {e}", exc_info=True)
  1955. if 'progress' in locals():
  1956. progress.close()
  1958. QMessageBox.critical(
  1959. self,
  1960. "Processing Error",
  1961. f"An error occurred during processing:\n\n{str(e)}\n\n"
  1962. f"Check the log file (plasticity_analyzer.log) for details."
  1963. )
  1965. self._update_ui_after_processing(success=False)
  1968. def _validate_processing_parameters(self) -> bool:
  1969. """
  1970. Validate all parameters before processing.
  1972. Checks:
  1973. - Image is loaded
  1974. - ROI is defined (minimum 3 vertices)
  1975. - ROI area is positive
  1976. - Z range is valid
  1977. - Voxel sizes are positive
  1979. Returns
  1980. -------
  1981. bool
  1982. True if all parameters are valid, False otherwise
  1984. Notes
  1985. -----
  1986. Displays warning dialogs for validation failures
  1987. """
  1988. # Check if image is loaded
  1989. if not hasattr(self, 'complexity_channel') or self.complexity_channel is None:
  1990. QMessageBox.warning(self, "No Image", "Please load an image first.")
  1991. return False
  1993. # Check if ROI is defined
  1994. if not hasattr(self, 'polygon_points') or len(self.polygon_points) < 3:
  1995. QMessageBox.warning(
  1996. self,
  1997. "No ROI",
  1998. "Please define a Region of Interest (ROI) first.\n"
  1999. "Click 'Select ROI' and draw a polygon around the structure."
  2000. )
  2001. return False
  2003. # Check if ROI area was calculated
  2004. if not hasattr(self, 'AArea') or self.AArea <= 0:
  2005. QMessageBox.warning(
  2006. self,
  2007. "Invalid ROI",
  2008. "ROI area is zero. Please redraw the ROI."
  2009. )
  2010. return False
  2012. # Validate Z range
  2013. z_start = self.ui.spinBox_zmin.value()
  2014. z_end = self.ui.spinBox_zmax.value()
  2016. if z_start >= z_end:
  2017. QMessageBox.warning(
  2018. self,
  2019. "Invalid Z Range",
  2020. f"Z start ({z_start}) must be less than Z end ({z_end})."
  2021. )
  2022. return False
  2024. if z_end > self.complexity_channel.shape[0]:
  2025. QMessageBox.warning(
  2026. self,
  2027. "Invalid Z Range",
  2028. f"Z end ({z_end}) exceeds image depth "
  2029. f"({self.complexity_channel.shape[0]})."
  2030. )
  2031. return False
  2033. # Validate voxel sizes
  2034. try:
  2035. voxel_x = float(self.ui.lineEdit_pixel_size_X.text())
  2036. voxel_y = float(self.ui.lineEdit_pixel_size_Y.text())
  2037. voxel_z = float(self.ui.lineEdit_pixel_size_Z.text())
  2039. if voxel_x <= 0 or voxel_y <= 0 or voxel_z <= 0:
  2040. QMessageBox.warning(
  2041. self,
  2042. "Invalid Voxel Size",
  2043. "All voxel sizes must be positive numbers."
  2044. )
  2045. return False
  2047. except ValueError:
  2048. QMessageBox.warning(
  2049. self,
  2050. "Invalid Voxel Size",
  2051. "Please enter valid numeric values for voxel sizes."
  2052. )
  2053. return False
  2055. logger.info("✓ All parameters validated")
  2056. return True
  2059. def _prepare_masked_images(
  2060. self,
  2061. z_start: int,
  2062. z_end: int
  2063. ) -> Tuple[Optional[np.ndarray], Optional[np.ndarray]]:
  2064. """
  2065. Prepare masked images for complexity and fluorescence channels.
  2067. This method:
  2068. 1. Extracts Z-slice subset
  2069. 2. Returns already-masked images (mask was applied in apply_roi_mask)
  2071. Parameters
  2072. ----------
  2073. z_start : int
  2074. Starting Z slice (inclusive)
  2075. z_end : int
  2076. Ending Z slice (inclusive)
  2078. Returns
  2079. -------
  2080. Tuple[Optional[np.ndarray], Optional[np.ndarray]]
  2081. (masked_complexity, masked_fluor)
  2082. - masked_complexity: Masked plasticity channel
  2083. - masked_fluor: Masked fluorescence channel (None if not selected)
  2084. Returns (None, None) if preparation fails
  2086. Notes
  2087. -----
  2088. - Images are already masked (apply_roi_mask was called earlier)
  2089. - Only Z-range extraction is performed here
  2090. - Logs intensity statistics for verification
  2091. """
  2092. try:
  2093. logger.info("Preparing masked images...")
  2095. # Extract Z-range from complexity channel
  2096. complexity_subset = self.complexity_channel[z_start:z_end+1, :, :]
  2097. logger.info(f"Complexity channel shape: {complexity_subset.shape}")
  2098. logger.info(f"Intensity: {np.sum(complexity_subset):.2f}, "
  2099. f"Non-zero: {np.count_nonzero(complexity_subset)}")
  2101. # Extract Z-range from fluorescence channel (if exists)
  2102. fluor_subset = None
  2103. if self.fluor_channel is not None:
  2104. fluor_subset = self.fluor_channel[z_start:z_end+1, :, :]
  2105. logger.info(f"Fluorescence channel shape: {fluor_subset.shape}")
  2107. return complexity_subset, fluor_subset
  2109. except Exception as e:
  2110. logger.error(f"Error preparing masked images: {e}", exc_info=True)
  2111. QMessageBox.critical(
  2112. self,
  2113. "Mask Error",
  2114. f"Failed to prepare images:\n{str(e)}"
  2115. )
  2116. return None, None
  2119. def _plot_distributions(
  2120. self,
  2121. MMsum: np.ndarray,
  2122. MMyy: np.ndarray,
  2123. MMzz: np.ndarray
  2124. ):
  2125. """
  2126. Plot X, Y, Z distributions for visual inspection.
  2128. Creates a 3-panel figure showing:
  2129. - Intensity distribution along X (horizontal)
  2130. - Y-spread at each X position
  2131. - Z-spread at each X position
  2133. Parameters
  2134. ----------
  2135. MMsum : np.ndarray
  2136. Intensity sum at each X position
  2137. MMyy : np.ndarray
  2138. Local Y-variance at each X position
  2139. MMzz : np.ndarray
  2140. Local Z-variance at each X position
  2142. Notes
  2143. -----
  2144. - Plots are shown in a matplotlib window
  2145. - User must close window to continue
  2146. - Useful for quality control and troubleshooting
  2147. """
  2148. try:
  2149. fig, axs = plt.subplots(1, 3, figsize=(15, 4))
  2151. # X distribution (intensity)
  2152. axs[0].plot(MMsum, linewidth=2, color='#2E86AB')
  2153. axs[0].set_title(
  2154. 'Intensity Along X (Horizontal)',
  2155. fontsize=14,
  2156. fontweight='bold'
  2157. )
  2158. axs[0].set_xlabel('X Position (pixels)', fontsize=12)
  2159. axs[0].set_ylabel('Intensity Sum', fontsize=12)
  2160. axs[0].grid(True, alpha=0.3)
  2161. axs[0].set_facecolor('#F8F9FA')
  2163. # Y distribution (variance)
  2164. axs[1].plot(MMyy, linewidth=2, color='#F18F01')
  2165. axs[1].set_title('Y-Spread at Each X', fontsize=14, fontweight='bold')
  2166. axs[1].set_xlabel('X Position (pixels)', fontsize=12)
  2167. axs[1].set_ylabel('Variance (pixels²)', fontsize=12)
  2168. axs[1].grid(True, alpha=0.3)
  2169. axs[1].set_facecolor('#F8F9FA')
  2171. # Z distribution (variance)
  2172. axs[2].plot(MMzz, linewidth=2, color='#06A77D')
  2173. axs[2].set_title('Z-Spread at Each X', fontsize=14, fontweight='bold')
  2174. axs[2].set_xlabel('X Position (pixels)', fontsize=12)
  2175. axs[2].set_ylabel('Variance (slices²)', fontsize=12)
  2176. axs[2].grid(True, alpha=0.3)
  2177. axs[2].set_facecolor('#F8F9FA')
  2179. plt.suptitle('Distribution Analysis', fontsize=16, fontweight='bold', y=1.02)
  2180. plt.tight_layout()
  2181. plt.show()
  2183. logger.info("Distribution plots displayed")
  2185. except Exception as e:
  2186. logger.warning(f"Failed to plot distributions: {e}")
  2189. def _save_results_to_csv(self, results: dict):
  2190. """
  2191. Save processing results to CSV file.
  2193. Appends a new row with:
  2194. - Image filename
  2195. - Spread metrics (pixels and µm)
  2196. - Axonal volume
  2197. - Fluorescence values
  2198. - User observation/notes
  2200. Parameters
  2201. ----------
  2202. results : dict
  2203. Processing results from ImageProcessor
  2205. Notes
  2206. -----
  2207. - CSV file path was set during load_images()
  2208. - Observation text is taken from UI text edit widget
  2209. - Results are appended to existing CSV (does not overwrite)
  2210. """
  2211. try:
  2212. if not hasattr(self, 'csv_file_path') or not self.csv_file_path:
  2213. logger.error("No CSV file path defined")
  2214. QMessageBox.warning(
  2215. self,
  2216. "No Output File",
  2217. "Output CSV file is not defined."
  2218. )
  2219. return
  2221. observation = self.ui.textEdit_observation.toPlainText()
  2222. image_name = os.path.basename(self.current_image_filepath)
  2224. # Write to CSV
  2225. with open(self.csv_file_path, mode='a', newline='', encoding='utf-8') as csv_file:
  2226. writer = csv.writer(csv_file)
  2227. writer.writerow([
  2228. image_name,
  2229. results['spread_x_pixel'],
  2230. results['spread_y_pixel'],
  2231. results['spread_z_pixel'],
  2232. results['spread_xy_pixel'],
  2233. results['spread_xyz_pixel'],
  2234. results['spread_x_um'],
  2235. results['spread_y_um'],
  2236. results['spread_z_um'],
  2237. results['spread_xy_um'],
  2238. results['spread_xyz_um'],
  2239. results['axonal_volume'],
  2240. results['fluorescence_px'],
  2241. results['fluorescence_um'],
  2242. f'"{observation}"'
  2243. ])
  2245. logger.info(f"✓ Results saved to: {self.csv_file_path}")
  2247. except Exception as e:
  2248. logger.error(f"Error saving results: {e}", exc_info=True)
  2249. QMessageBox.critical(
  2250. self,
  2251. "Save Error",
  2252. f"Failed to save results to CSV:\n{str(e)}"
  2253. )
  2256. def _update_ui_after_processing(self, success: bool = True):
  2257. """
  2258. Update UI elements after processing.
  2260. Parameters
  2261. ----------
  2262. success : bool, optional
  2263. Whether processing was successful (default: True)
  2265. UI Updates
  2266. ----------
  2267. - Mark processed image in list:
  2268. - Green background: Success
  2269. - Red background: Error
  2270. - Update status bar (if available)
  2272. Notes
  2273. -----
  2274. Errors in UI update are logged but do not interrupt workflow
  2275. """
  2276. try:
  2277. # Mark processed image in list
  2278. selected_items = self.ui.listWidget_images.selectedItems()
  2279. if selected_items:
  2280. if success:
  2281. selected_items[0].setBackground(pyqtgraph.mkColor('lightgreen'))
  2282. else:
  2283. selected_items[0].setBackground(pyqtgraph.mkColor("#FB889A"))
  2285. # Update status bar if exists
  2286. if hasattr(self, 'statusBar'):
  2287. if success:
  2288. self.statusBar().showMessage("✓ Processing completed", 5000)
  2289. else:
  2290. self.statusBar().showMessage("✗ Processing failed", 5000)
  2292. except Exception as e:
  2293. logger.warning(f"Failed to update UI: {e}")
  2296. # ========================================================================
  2297. # APPLICATION ENTRY POINT
  2298. # ========================================================================
  2300. if __name__ == "__main__":
  2301. app = QApplication(sys.argv)
  2302. window = MyMainWindow()
  2303. window.show()
  2304. sys.exit(app.exec())

MorphoScope.py at commit 6cb847b, under MIT · at the source

Overview

Authors: Athira Theyyassanchery Mani1, Vivian Backs1, Christian Werner2, Charlotte Helfrich-Förster3, Thomas Raabe1
ORCID iDs: Athira Theyyassanchery Mani, Charlotte Helfrich-Förster, Thomas Raabe
  1. Molecular Genetics, Biocenter, University of Würzburg, Würzburg, Germany
  2. Biotechnology and Biophysics, Biocenter, University of Würzburg, Würzburg, Germany
  3. Neurobiology and Genetics, Biocenter, University of Würzburg, Würzburg, Germany
Institutions: University of Würzburg (Germany)
Journal: Journal of biological rhythms, volume 41, issue 4, pages 416-434
Dates: published online 12 April 2026; in print August 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1177/07487304261434715 · PMID 41966995 · PMCID PMC13342480 · OpenAlex W7153884631
Open access: hybrid, a free copy (OpenAlex)
Status: code verified
Categories: drosophila (organism), cellular / molecular (subfield)
Methods: Statistics, Evoked potentials, fMRI & imaging
Keywords: Drosophila, clock neurons, structural plasticity, circadian rhythm, adaptation
MeSH: Behavior, Animal*, Circadian Rhythm*, Drosophila*, Drosophila melanogaster*, Drosophila Proteins*, Neuronal Plasticity*, Neurons*, Ribosomal Protein S6 Kinases*, Ribosomal Protein S6 Kinases, 70-kDa*, Animals, Mutation, Ribosomal Protein S6 Kinases, 90-kDa (* major topic)
Topic: Circadian rhythm and melatonin (Endocrine and Autonomic Systems, Neuroscience), according to OpenAlex
Funding: Deutsche Forschungsgemeinschaft (Fo207-19/1, Ra561-11/1)
Citations: cited by 2 papers (Europe PMC); 83 references in the paper

Abstract

Circadian neuronal plasticity describes daily recurring changes at the level of neuronal morphology, connectivity and synaptic processes. Disturbance of these plastic changes could result in inflexibility of an organism to adapt behavior to changing environmental cues. The mitogen activated protein kinases (MAPK)/ERK signaling pathway is involved both in circadian processes and neuronal plasticity. Ribosomal S6 kinases (RSK) act as downstream mediators of ERK signaling with apparently pleiotropic—but sometimes poorly understood- functions in the nervous system. This is illustrated by some major gaps in our understanding of the pathophysiological processes caused by RSK2 mutations in humans that lead to intellectual disabilities. Previous studies described the role of Drosophila RSK as one regulator of the molecular circadian oscillator. Here we could show that RSK kinase activity is required to control another aspect of circadian rhythmicity, the daily remodeling of the dorsal branching pattern of the small ventral lateral neurons (s-LNv) as the central pacemaker cells. Loss of RSK function resulted in more fasciculated and less branched s-LNv’s in the early morning, which could affect synaptic in- or output connectivity. Increased fasciculation correlated with a reduced number of Bruchpilot sites as a marker for presynapses. Analysis of the expression of the Pigment Dispersing Factor PDF in s-LNv’s, the most important signaling factor between clock neurons, revealed no evidence of changes in RSK mutants. Consistent with unaffected PDF signaling as a major output from the s-LNv’s, RSK mutant flies are rhythmic. Their free-running rhythms show even a significantly higher power than those of the wild-type controls. This robustness is at the expense of flexibility to adapt their activity to variations in light conditions. Together with the known role of RSK in olfactory learning and memory processes our results suggest that RSK is required to maintain experience dependent plasticity.

Reproduced under the paper's license (CC BY), from the paper cited above.

Repository

Its files are read in the Code ↔ Paper reader above, with 1 match between paragraphs and lines of code.

FranTassara/MorphoScope

License: MIT
State: the link answers, verified on 26 September 2026
Evidence: files inventoried
Commit: 6cb847ba76bdaeab3d8ba2b247e8ce269cde485c, 16 July 2026
Languages: Python (4)
Size: 15 files, 4 scripts
Software Heritage: not archived
Found in: the text, “Quantification of s-LN v Arborization”
Holds: README, license file, CITATION.cff, environment (requirements.txt)
Not found: tests, continuous integration, documentation
Tools: NumPy (3 files), Matplotlib (2 files), SciPy (2 files), tifffile (2 files), scikit-image (1 file)
Availability: 1 check, the latest on 26 September 2026: the link answers
  • 26 September 2026: the link answers
6 files
At the source: github.com/FranTassara/MorphoScope

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 4 scripts, each with its path and the digest of its content;
  • 1 match between paragraphs of the paper and lines of the code (method lexical-v1);
  • neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

No dataset and no data link were found in the paper.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 1, 29 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 5 authors, 5 keywords, 12 MeSH terms, 1 funder, 83 references.

Cite

This paper

Theyyassanchery Mani, A., Backs, V., Werner, C., Helfrich-Förster, C., & Raabe, T. (2026). &lt;i&gt;Drosophila&lt;/i&gt; RSK: A Pivotal Regulator of Circadian Plasticity at the Neuronal and Behavioral Level. Journal of biological rhythms, 41(4), 416-434. https://doi.org/10.1177/07487304261434715

BibTeX

@article{theyyassancherymani2026lt,
author = {Theyyassanchery Mani, Athira and Backs, Vivian and Werner, Christian and Helfrich-Förster, Charlotte and Raabe, Thomas},
title = {{\&lt;i\&gt;Drosophila\&lt;/i\&gt; RSK: A Pivotal Regulator of Circadian Plasticity at the Neuronal and Behavioral Level}},
journal = {Journal of biological rhythms},
year = {2026},
month = apr,
volume = {41},
number = {4},
pages = {416--434},
publisher = {SAGE Publishing},
issn = {0748-7304},
doi = {10.1177/07487304261434715},
url = {https://doi.org/10.1177/07487304261434715},
pmid = {41966995},
pmcid = {PMC13342480}
}

RIS

TY - JOUR
AU - Theyyassanchery Mani, Athira
AU - Backs, Vivian
AU - Werner, Christian
AU - Helfrich-Förster, Charlotte
AU - Raabe, Thomas
TI - &lt;i&gt;Drosophila&lt;/i&gt; RSK: A Pivotal Regulator of Circadian Plasticity at the Neuronal and Behavioral Level
T2 - Journal of biological rhythms
J2 - J Biol Rhythms
PY - 2026
DA - 2026/04/12
VL - 41
IS - 4
SP - 416
EP - 434
SN - 0748-7304
PB - SAGE Publishing
DO - 10.1177/07487304261434715
UR - https://doi.org/10.1177/07487304261434715
LA - en
ER -

CSL-JSON

{
"id": "10.1177/07487304261434715",
"type": "article-journal",
"title": "&lt;i&gt;Drosophila&lt;/i&gt; RSK: A Pivotal Regulator of Circadian Plasticity at the Neuronal and Behavioral Level",
"container-title": "Journal of biological rhythms",
"author": [
{
"family": "Theyyassanchery Mani",
"given": "Athira"
},
{
"family": "Backs",
"given": "Vivian"
},
{
"family": "Werner",
"given": "Christian"
},
{
"family": "Helfrich-Förster",
"given": "Charlotte"
},
{
"family": "Raabe",
"given": "Thomas"
}
],
"container-title-short": "J Biol Rhythms",
"volume": "41",
"issue": "4",
"page": "416-434",
"DOI": "10.1177/07487304261434715",
"PMID": "41966995",
"PMCID": "PMC13342480",
"ISSN": "0748-7304",
"publisher": "SAGE Publishing",
"URL": "https://doi.org/10.1177/07487304261434715",
"language": "en",
"issued": {
"date-parts": [
[
2026,
4,
12
]
]
}
}

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