OSCR

Protocol for semi-automatic quantitative bioimaging analysis of synapse loss.

Code ↔ Paper

2 matches 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 2 matches
  1. [1] § Step-by-step method details › Install Fiji, plugins, and macros ↔ src/main/java/fiji/plugin/ComDet/CDDialog.java, lines 120–182 · score 0.57 · Max distance, colocalized spots, ComDet, dialog, Install, plugins
  2. [2] § Step-by-step method details › Install Fiji, plugins, and macros ↔ src/main/java/fiji/plugin/ComDet/Detect_Particles.java, lines 912–970 · score 0.53 · Max distance, colocalized spots, ComDet, plugins, Fiji

Paper

Loaded from Europe PMC by your browser, not stored by OSCR: doi.org · Europe PMC

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The authors' code

Java · 385 lines · 11 KB · GPL-3.0 · 1 match

  1. /*-
  2. * #%L
  3. * ComDet Plugin for ImageJ
  4. * %%
  5. * Copyright (C) 2012 - 2025 Cell Biology, Neurobiology and Biophysics
  6. * Department of Utrecht University.
  7. * %%
  8. * This program is free software: you can redistribute it and/or modify
  9. * it under the terms of the GNU General Public License as
  10. * published by the Free Software Foundation, either version 3 of the
  11. * License, or (at your option) any later version.
  12. *
  13. * This program is distributed in the hope that it will be useful,
  14. * but WITHOUT ANY WARRANTY; without even the implied warranty of
  15. * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
  16. * GNU General Public License for more details.
  17. *
  18. * You should have received a copy of the GNU General Public
  19. * License along with this program. If not, see
  20. * <http://www.gnu.org/licenses/gpl-3.0.html>.
  21. * #L%
  22. */
  23. package fiji.plugin.ComDet;
  25. import java.awt.AWTEvent;
  26. import java.awt.Color;
  28. import ij.CompositeImage;
  29. import ij.IJ;
  30. import ij.ImagePlus;
  31. import ij.Prefs;
  32. import ij.gui.DialogListener;
  33. import ij.gui.GenericDialog;
  34. import ij.gui.Overlay;
  35. import ij.gui.Roi;
  36. import ij.process.FloatProcessor;
  37. import ij.process.ImageProcessor;
  40. public class CDDialog implements DialogListener{
  43. /** current active ImagePlus **/
  44. public ImagePlus imp;
  47. CDAnalysis cd;
  48. /**image width of original image**/
  49. int nWidth;
  50. /**image height of original image**/
  51. int nHeight;
  52. /**number of slices**/
  53. int nSlices;
  55. /** original overlay **/
  56. Overlay savedOverlay;
  59. //finding particles
  60. /**standard deviation of PSF approximated by Gaussian**/
  61. double [] dPSFsigma;
  62. /**size of Gaussian kernel for particles enhancement**/
  63. int [] nKernelSize;
  64. /**number of threads for calculation**/
  65. int nThreads;
  66. /**threshold of minimum particle area for each channel **/
  67. int [] nAreaCut;
  68. /**threshold of maximum particle area for each channel **/
  69. int [] nAreaMax;
  70. /**sensitivity of detection for each channel **/
  71. float [] nSensitivity;
  72. /** whether to include big particles in the detection (for each channel) **/
  73. boolean [] bBigParticles;
  74. /** Whether to segment large particles (for each channel) **/
  75. boolean [] bSegmentLargeParticles;
  76. /** ROI of what shape to add 0 = ovals, 1 = rectangles **/
  77. int nRoiOption;
  79. /** number of channels **/
  80. public int ChNumber;
  81. /** current channel in processing (starting from 1!) **/
  82. int iCh;
  84. /** main dialog window **/
  85. GenericDialog fpDial;
  87. boolean bMultiChannelDetection;
  91. /** dialog options**/
  92. String [] sROIManagerOneCh;
  93. String [] sROIManagerMultiCh;
  95. String [] sSummaryOptions;
  96. /** 0 reset summary table; 1 append to a summary table **/
  97. int nSummaryOptions;
  99. /** Flag determing whether to add detections to ROI Manager
  100. * 0 - do not add
  101. * 1 - add all detections
  102. * 2 - add only colocalized particles
  103. * 3 - add only non-colocalized particles
  104. * **/
  105. int nRoiManagerAdd;
  106. /** ROIs of what shape to add **/
  107. String [] sRoiOptions;
  110. //boolean bPreview;
  113. //colocalization analysis parameters
  114. boolean bColocalization;
  115. double dColocDistance;
  116. boolean bPlotMultiChannels;
  117. boolean bJoinROIs;
  120. /** default constructor **/
  121. public CDDialog()
  122. {
  123. //dPSFsigma = new double[2];
  124. //nKernelSize = new int[2];
  125. //nAreaCut = new int[2];
  126. //nAreaMax = new int[2];
  127. //nSensitivity = new float[2];
  128. sROIManagerOneCh = new String [] {
  129. "Nothing", "All detections"};
  130. sROIManagerMultiCh = new String [] {
  131. "Nothing", "All detections","Only colocalized particles", "Only non-colocalized particles"};
  132. sRoiOptions = new String [] {"Ovals","Rectangles"};
  134. sSummaryOptions =new String [] {"Reset","Append"};
  136. }
  137. /** function initializing dialog for particles detection,
  138. * reads parameters of current image (or Stack/HyperStack, etc) **/
  139. public void initImage(ImagePlus imp_in, int [] imageinfo_in)
  140. {
  141. imp=imp_in;
  142. ChNumber=imageinfo_in[2];
  143. dPSFsigma = new double[ChNumber];
  144. nKernelSize = new int[ChNumber];
  145. nAreaCut = new int[ChNumber];
  146. nAreaMax = new int[ChNumber];
  147. nSensitivity = new float[ChNumber];
  148. bBigParticles = new boolean[ChNumber];
  149. bSegmentLargeParticles = new boolean[ChNumber];
  151. }
  153. //dialog showing options for particle search algorithm
  154. public boolean findParticles() {
  156. String nCurrentVersion;
  159. //check if it is new version
  160. // if yes, display one time message
  161. nCurrentVersion=Prefs.get("ComDet.PluginVersion","none");
  162. if(!nCurrentVersion.equals(ComDetConstants.ComDetVersion))
  163. {
  164. IJ.showMessage("This is a new installation or an update to "+ComDetConstants.ComDetVersion+" version of ComDet plugin!\n "
  165. //+ "Take notice that detection algorithm has changed in comparison to previous versions.\n"
  166. +"Check https://github.com/ekatrukha/ComDet/wiki/Updates-history for description of changes. ");
  167. Prefs.set("ComDet.PluginVersion",ComDetConstants.ComDetVersion);
  168. }
  170. //multichannel input, ask user for the parameters
  171. if(ChNumber > 1)
  172. {
  173. fpDial = new GenericDialog("Detect Particles");
  174. fpDial.addMessage("Multi-channel image is detected as input. \n");
  175. fpDial.addCheckbox("Calculate colocalization?", Prefs.get("ComDet.bColocalization", false));
  176. fpDial.addMessage("Colocalization analysis parameters:\n");
  177. fpDial.addNumericField("Max distance between colocalized spots", Prefs.get("ComDet.dColocDistance", 4), 2,5," pixels");
  178. fpDial.addCheckbox( "Join ROIs for intensity of colocalized particles", Prefs.get("ComDet.bJoinROIs", true) );
  179. fpDial.addCheckbox("Plot detected particles in all channels?", Prefs.get("ComDet.bPlotMultiChannels", false));
  180. fpDial.addChoice("ROIs shape: ",sRoiOptions, Prefs.get("ComDet.nRoiOption", "Ovals"));
  181. fpDial.addChoice("Add to ROI Manager:", sROIManagerMultiCh, Prefs.get("ComDet.sROIManagerMulti", "Nothing"));
  182. fpDial.addChoice("Summary Table:", sSummaryOptions, Prefs.get("ComDet.sSummaryOptions", "Reset"));
  185. fpDial.showDialog();
  186. if (fpDial.wasCanceled())
  187. return false;
  188. bColocalization = fpDial.getNextBoolean();
  189. Prefs.set("ComDet.bColocalization", bColocalization);
  191. dColocDistance = fpDial.getNextNumber();
  192. Prefs.set("ComDet.dColocDistance", dColocDistance);
  194. bJoinROIs = fpDial.getNextBoolean();
  195. Prefs.set("ComDet.bJoinROIs", bJoinROIs);
  197. bPlotMultiChannels = fpDial.getNextBoolean();
  198. Prefs.set("ComDet.bPlotMultiChannels", bPlotMultiChannels);
  200. nRoiOption = fpDial.getNextChoiceIndex();
  201. Prefs.set("ComDet.nRoiOption", sRoiOptions[nRoiOption]);
  203. nRoiManagerAdd = fpDial.getNextChoiceIndex();
  204. Prefs.set("ComDet.sROIManagerMulti", sROIManagerMultiCh[nRoiManagerAdd]);
  206. nSummaryOptions = fpDial.getNextChoiceIndex();
  207. Prefs.set("ComDet.sSummaryOptions", sSummaryOptions[nSummaryOptions]);
  209. if(!bColocalization && nRoiManagerAdd>=2)
  210. {
  211. nRoiManagerAdd=0;
  212. IJ.log("Cannot add colocalized particles to ROI, since colocalization option is unchecked. Nothing will be added.");
  213. }
  214. Prefs.set("ComDet.sROIManagerMultiCh", sROIManagerMultiCh[nRoiManagerAdd]);
  215. }
  217. savedOverlay = imp.getOverlay();
  220. for (iCh=1;iCh<=ChNumber;iCh++)
  221. {
  222. String sChN = Integer.toString(iCh);
  223. fpDial = new GenericDialog("Detect Particles channel"+sChN);
  224. fpDial.addMessage("Detection parameters:\n");
  225. fpDial.addCheckbox("ch"+sChN+"i: Include larger particles?", Prefs.get("ComDet.bBigParticles"+sChN, true));
  226. fpDial.addCheckbox("ch"+sChN+"l: Segment larger particles (slow)?", Prefs.get("ComDet.bSegmentLargeParticles"+sChN, false));
  227. fpDial.addNumericField("ch"+sChN+"a: Approximate particle size", Prefs.get("ComDet.dPSFsigma"+sChN, 4), 2,5," pixels");
  228. fpDial.addNumericField("ch"+sChN+"s: Intensity threshold (in SD):", Prefs.get("ComDet.dSNRT"+sChN, 3), 2,5, "around (3-20)");
  229. if(ChNumber == 1)
  230. {
  231. fpDial.addChoice("ROIs shape: ",sRoiOptions, Prefs.get("ComDet.nRoiOption", "Ovals"));
  232. fpDial.addChoice("Add to ROI Manager:", sROIManagerOneCh, Prefs.get("ComDet.sROIManagerOne", "Nothing"));
  233. fpDial.addChoice("Summary Table:", sSummaryOptions, Prefs.get("ComDet.sSummaryOptions", "Reset"));
  234. }
  236. ImagePlus fakeimp=new ImagePlus("quick",new FloatProcessor(1,1));
  237. fakeimp.show();
  238. fpDial.addPreviewCheckbox(null,"Preview detection..");
  239. fakeimp.changes=false;
  240. fakeimp.close();
  241. fpDial.addDialogListener(this);
  243. fpDial.showDialog();
  245. imp.setOverlay(savedOverlay);
  246. imp.updateAndRepaintWindow();
  247. imp.show();
  249. if (fpDial.wasCanceled())
  250. {return false;}
  252. setPrefs();
  254. }
  258. return true;
  259. }
  261. @Override
  262. public boolean dialogItemChanged(GenericDialog gd, AWTEvent e) {
  263. // TODO Auto-generated method stub
  265. CompositeImage multichannel_imp;
  266. int[] nImagePos;
  267. Roi RoiSelected;// = imp.getRoi();
  268. ImageProcessor ip;
  269. boolean bValuesOk;
  270. bValuesOk=getValues();
  271. if(!bValuesOk)
  272. return false;
  273. if(gd.wasOKed())
  274. {
  275. return true;
  276. }
  277. if(gd.isPreviewActive())
  278. {
  279. gd.previewRunning(true);
  280. cd = new CDAnalysis(ChNumber);
  282. if(ChNumber>1)
  283. {
  284. multichannel_imp=(CompositeImage) imp;
  285. multichannel_imp.setC(iCh);
  286. cd.colorCh= multichannel_imp.getChannelColor();
  287. }
  288. else
  289. {
  290. cd.colorCh=Color.YELLOW;
  291. }
  293. cd.overlay_= new Overlay();
  294. cd.initConvKernel(this,iCh-1);
  295. RoiSelected= imp.getRoi();
  296. //nImagePos = imp.convertIndexToPosition(imp.getSlice());
  297. nImagePos = new int[3];
  298. nImagePos[0]=iCh;
  299. nImagePos[1]=imp.getSlice();
  300. nImagePos[2]=imp.getFrame();
  301. imp.setPositionWithoutUpdate(nImagePos[0], nImagePos[1],nImagePos[2]);
  302. ip = imp.getProcessor().duplicate();
  304. cd.detectParticles(ip, this,nImagePos, 1, RoiSelected);
  305. imp.setOverlay(cd.overlay_);
  306. imp.updateAndRepaintWindow();
  307. imp.show();
  308. gd.previewRunning(false);
  310. }
  311. else
  312. {
  313. imp.setOverlay(savedOverlay);
  314. imp.updateAndRepaintWindow();
  315. imp.show();
  316. }
  317. return true;
  318. }
  321. /** function reads parameters values from the dialog **/
  322. public boolean getValues()
  323. {
  324. int indCh=iCh-1;
  326. bBigParticles[indCh] = fpDial.getNextBoolean();
  327. bSegmentLargeParticles[indCh] = fpDial.getNextBoolean();
  329. dPSFsigma[indCh] = fpDial.getNextNumber();
  330. if(Double.isNaN(dPSFsigma[indCh]))
  331. return false;
  333. nSensitivity[indCh] = (float)fpDial.getNextNumber();
  334. if(Double.isNaN(nSensitivity[indCh]))
  335. return false;
  339. if(ChNumber == 1)
  340. {
  341. nRoiOption = fpDial.getNextChoiceIndex();
  342. nRoiManagerAdd = fpDial.getNextChoiceIndex();
  343. nSummaryOptions = fpDial.getNextChoiceIndex();
  345. }
  346. //bPreview = fpDial.getNextBoolean();
  347. nThreads = 50;
  350. dPSFsigma[indCh] *= 0.5;
  351. nAreaMax[indCh] = (int) (12.0*dPSFsigma[indCh]*dPSFsigma[indCh]);
  352. //putting limiting criteria on spot size
  353. nAreaCut[indCh] = (int) (dPSFsigma[indCh] * dPSFsigma[indCh]);
  354. nKernelSize[indCh] = (int) Math.ceil(3.0*dPSFsigma[indCh]);
  355. if(nKernelSize[indCh]%2 == 0)
  356. nKernelSize[indCh]++;
  358. return true;
  360. }
  363. /** function adds parameters values to registry **/
  364. public void setPrefs()
  365. {
  366. String sChN = Integer.toString(iCh);
  367. Prefs.set("ComDet.bBigParticles"+sChN, bBigParticles[iCh-1]);
  368. Prefs.set("ComDet.bSegmentLargeParticles"+sChN, bSegmentLargeParticles[iCh-1]);
  370. Prefs.set("ComDet.dPSFsigma"+sChN, dPSFsigma[iCh-1]*2.0);
  371. Prefs.set("ComDet.dSNRT"+sChN, nSensitivity[iCh-1]);
  373. if(ChNumber == 1)
  374. {
  375. Prefs.set("ComDet.sROIManagerOne", sROIManagerOneCh[nRoiManagerAdd]);
  376. }
  377. Prefs.set("ComDet.sSummaryOptions", sSummaryOptions[nSummaryOptions]);
  379. Prefs.set("ComDet.nRoiOption", sRoiOptions[nRoiOption]);
  381. //Prefs.set("ComDet.bPreview", bPreview);
  382. }
  385. }

CDDialog.java at commit cda3eb7, under GPL-3.0 · at the source

Overview

Authors: Mariana A Barata1, Cláudia Guimas Almeida1
ORCID iDs: Mariana A Barata, Cláudia Guimas Almeida
  1. iNOVA4Health, NOVA Medical School, Universidade NOVA de Lisboa, 1169-056 Lisboa, Portugal
Institutions: Universidade Nova de Lisboa (Portugal)
Journal: STAR protocols, volume 7, issue 3, article 104675
Dates: published online 3 July 2026; in print July 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1016/j.xpro.2026.104675 · PMID 42397748 · PMCID PMC13355525 · OpenAlex W7167255126
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: histology / microscopy (modality), cellular / molecular (subfield)
Methods: Statistics, Evoked potentials, fMRI & imaging
Keywords: Cell-based Assays, Microscopy, Neuroscience
Topic: Advanced Fluorescence Microscopy Techniques (Biophysics, Biochemistry, Genetics and Molecular Biology), according to OpenAlex
Funding: Ministério da Educação e Ciência; European Regional Development Fund; Foundation for Science and Technology
Citations: not cited yet (Europe PMC); 23 references in the paper
Research resources: Chicken polyclonal anti-MAP2 1:500 (IF) RRID:AB_2138153, RRID:AB_2301998, RRID:AB_309738, RRID:AB_887878, pMD2.G RRID:Addgene_12259, psPAX2 RRID:Addgene_12260, STAR-RDpro RRID:CVCL_AR78, E16 pregnant females’ mice (BALB/c) RRID:IMSR_JAX:001026, Fiji (version 1.53) RRID:SCR_002285, GraphPad (version 8.4.0) RRID:SCR_002798

Abstract

The abstract is not reproduced here: the paper's license (CC BY-NC-ND) does not allow it. Read it in the paper, at the publisher or on Europe PMC.

Repositories

Its files are read in the Code ↔ Paper reader above, with 2 matches between paragraphs and lines of code.

ekatrukha/ComDet

License: GPL-3.0
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: cda3eb76a6da33583bd35d42402474e464c9c110, 16 June 2025
Languages: Java (16), Shell (2)
Size: 25 files, 18 scripts
Software Heritage: not archived
Found in: the resources table
Holds: README, license file, continuous integration
Not found: CITATION.cff, environment file, tests, documentation
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
20 files
At the source: github.com/ekatrukha/ComDet

neuroagingandAD/Synapsepunctaanalysis

License: none: the authors keep all their rights
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: 02cb0811bfa34a376edb3eb55971da228b6ab66c, 21 March 2026
Size: 3 files, 0 scripts
Software Heritage: not archived
Found in: “Data and code availability”
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
1 file
At the source: github.com/neuroagingandAD/Synapsepunctaanalysis.git

The paper's code and data availability statement is in the Data section.

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:

  • 2 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 18 scripts, each with its path and the digest of its content;
  • 2 matches 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.

Code and data availability statement

The paper has a code and data availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:

Read it in the paper: doi.org/10.1016/j.xpro.2026.104675.

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, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 2 authors, 3 keywords, 3 funders, 23 references, 10 RRIDs.

Cite

This paper

Barata, M. A., & Guimas Almeida, C. (2026). Protocol for semi-automatic quantitative bioimaging analysis of synapse loss. STAR protocols, 7(3), 104675. https://doi.org/10.1016/j.xpro.2026.104675

BibTeX

@article{barata2026protocol,
author = {Barata, Mariana A and Guimas Almeida, Cláudia},
title = {{Protocol for semi-automatic quantitative bioimaging analysis of synapse loss}},
journal = {STAR protocols},
year = {2026},
month = jul,
volume = {7},
number = {3},
pages = {104675},
publisher = {Elsevier},
issn = {2666-1667},
doi = {10.1016/j.xpro.2026.104675},
url = {https://doi.org/10.1016/j.xpro.2026.104675},
pmid = {42397748},
pmcid = {PMC13355525}
}

RIS

TY - JOUR
AU - Barata, Mariana A
AU - Guimas Almeida, Cláudia
TI - Protocol for semi-automatic quantitative bioimaging analysis of synapse loss
T2 - STAR protocols
J2 - STAR Protoc
PY - 2026
DA - 2026/07/03
VL - 7
IS - 3
SP - 104675
SN - 2666-1667
PB - Elsevier
DO - 10.1016/j.xpro.2026.104675
UR - https://doi.org/10.1016/j.xpro.2026.104675
LA - en
ER -

CSL-JSON

{
"id": "10.1016/j.xpro.2026.104675",
"type": "article-journal",
"title": "Protocol for semi-automatic quantitative bioimaging analysis of synapse loss",
"container-title": "STAR protocols",
"author": [
{
"family": "Barata",
"given": "Mariana A"
},
{
"family": "Guimas Almeida",
"given": "Cláudia"
}
],
"container-title-short": "STAR Protoc",
"volume": "7",
"issue": "3",
"page": "104675",
"DOI": "10.1016/j.xpro.2026.104675",
"PMID": "42397748",
"PMCID": "PMC13355525",
"ISSN": "2666-1667",
"publisher": "Elsevier",
"URL": "https://doi.org/10.1016/j.xpro.2026.104675",
"language": "en",
"issued": {
"date-parts": [
[
2026,
7,
3
]
]
}
}

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