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PTEN regulates starburst amacrine cell dendrite morphology during development.

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Paper

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The authors' code

Python · 401 lines · 12 KB · GPL-3.0

  1. #man_pagesdcmd# -*- coding: utf-8 -*-
  2. #
  3. # Stimulus Program documentation build configuration file, created by
  4. # sphinx-quickstart on Thu Feb 04 11:17:06 2016.
  5. #
  6. # This file is execfile()d with the current directory set to its
  7. # containing dir.
  8. #
  9. # Note that not all possible configuration values are present in this
  10. # autogenerated file.
  11. #
  12. # All configuration values have a default; values that are commented out
  13. # serve to show the default.
  15. import sys
  16. import os
  18. # If extensions (or modules to document with autodoc) are in another directory,
  19. # add these directories to sys.path here. If the directory is relative to the
  20. # documentation root, use os.path.abspath to make it absolute, like shown here.
  21. user = os.environ.get('USERNAME')
  23. if user == 'Alex':
  24. sys.path.insert(0, os.path.abspath(r'C:\Users\Alex\Anaconda3\envs\stimprogram\Lib\site-packages'))
  25. elif user == 'bensivyer':
  26. sys.path.insert(0, os.path.abspath(r'C:\Users\bensivyer\Anaconda3\envs\sp_env\Lib\site-packages'))
  28. sys.path.insert(0, os.path.abspath(r'../../pyStim'))
  30. # -- General configuration ------------------------------------------------
  32. # If your documentation needs a minimal Sphinx version, state it here.
  33. #needs_sphinx = '1.0'
  35. # Add any Sphinx extension module names here, as strings. They can be
  36. # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
  37. # ones.
  38. extensions = [
  39. 'sphinx.ext.githubpages',
  40. 'sphinx.ext.autodoc',
  41. 'sphinx.ext.intersphinx',
  42. # 'sphinx.ext.mathjax',
  43. 'sphinx.ext.viewcode',
  44. # 'rst2pdf.pdfbuilder' # add rst2pdf to pipfile if want to try building PDFs
  45. ]
  47. # Add any paths that contain templates here, relative to this directory.
  48. templates_path = ['_templates']
  50. # The suffix(es) of source filenames.
  51. # You can specify multiple suffix as a list of string:
  52. # source_suffix = ['.rst', '.md']
  53. source_suffix = '.rst'
  55. # The encoding of source files.
  56. #source_encoding = 'utf-8-sig'
  58. # The master toctree document.
  59. master_doc = 'index'
  61. # General information about the project.
  62. project = u'pyStim'
  63. copyright = u'2017, Alexander Tomlinson'
  64. author = u'Alexander Tomlinson'
  66. # The version info for the project you're documenting, acts as replacement for
  67. # |version| and |release|, also used in various other places throughout the
  68. # built documents.
  69. #
  70. # The short X.Y version.
  71. version = u'1.1'
  72. # The full version, including alpha/beta/rc tags.
  73. release = u'1.1'
  75. # The language for content autogenerated by Sphinx. Refer to documentation
  76. # for a list of supported languages.
  77. #
  78. # This is also used if you do content translation via gettext catalogs.
  79. # Usually you set "language" from the command line for these cases.
  80. language = None
  82. # There are two options for replacing |today|: either, you set today to some
  83. # non-false value, then it is used:
  84. #today = ''
  85. # Else, today_fmt is used as the format for a strftime call.
  86. #today_fmt = '%B %d, %Y'
  88. # List of patterns, relative to source directory, that match files and
  89. # directories to ignore when looking for source files.
  90. exclude_patterns = []
  92. # The reST default role (used for this markup: `text`) to use for all
  93. # documents.
  94. #default_role = None
  96. # If true, '()' will be appended to :func: etc. cross-reference text.
  97. #add_function_parentheses = True
  99. # If true, the current module name will be prepended to all description
  100. # unit titles (such as .. function::).
  101. #add_module_names = True
  103. # If true, sectionauthor and moduleauthor directives will be shown in the
  104. # output. They are ignored by default.
  105. #show_authors = False
  107. # The name of the Pygments (syntax highlighting) style to use.
  108. pygments_style = 'sphinx'
  110. # A list of ignored prefixes for module index sorting.
  111. #modindex_common_prefix = []
  113. # If true, keep warnings as "system message" paragraphs in the built documents.
  114. #keep_warnings = False
  116. # If true, `todo` and `todoList` produce output, else they produce nothing.
  117. todo_include_todos = False
  120. # -- Options for HTML output ----------------------------------------------
  122. # The theme to use for HTML and HTML Help pages. See the documentation for
  123. # a list of builtin themes.
  124. html_theme = 'sphinxdoc'
  126. # Theme options are theme-specific and customize the look and feel of a theme
  127. # further. For a list of options available for each theme, see the
  128. # documentation.
  129. #html_theme_options = {}
  131. # Add any paths that contain custom themes here, relative to this directory.
  132. #html_theme_path = []
  134. # The name for this set of Sphinx documents. If None, it defaults to
  135. # "<project> v<release> documentation".
  136. #html_title = None
  138. # A shorter title for the navigation bar. Default is the same as html_title.
  139. #html_short_title = None
  141. # The name of an image file (relative to this directory) to place at the top
  142. # of the sidebar.
  143. #html_logo = None
  145. # The name of an image file (within the static path) to use as favicon of the
  146. # docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
  147. # pixels large.
  148. #html_favicon = None
  150. # Add any paths that contain custom static files (such as style sheets) here,
  151. # relative to this directory. They are copied after the builtin static files,
  152. # so a file named "default.css" will overwrite the builtin "default.css".
  153. # html_static_path = ['_static']
  155. # Add any extra paths that contain custom files (such as robots.txt or
  156. # .htaccess) here, relative to this directory. These files are copied
  157. # directly to the root of the documentation.
  158. #html_extra_path = []
  160. # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
  161. # using the given strftime format.
  162. #html_last_updated_fmt = '%b %d, %Y'
  164. # If true, SmartyPants will be used to convert quotes and dashes to
  165. # typographically correct entities.
  166. #html_use_smartypants = True
  168. # Custom sidebar templates, maps document names to template names.
  169. #html_sidebars = {}
  171. # Additional templates that should be rendered to pages, maps page names to
  172. # template names.
  173. #html_additional_pages = {}
  175. # If false, no module index is generated.
  176. #html_domain_indices = True
  178. # If false, no index is generated.
  179. #html_use_index = True
  181. # If true, the index is split into individual pages for each letter.
  182. #html_split_index = False
  184. # If true, links to the reST sources are added to the pages.
  185. #html_show_sourcelink = True
  187. # If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
  188. #html_show_sphinx = True
  190. # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
  191. #html_show_copyright = True
  193. # If true, an OpenSearch description file will be output, and all pages will
  194. # contain a <link> tag referring to it. The value of this option must be the
  195. # base URL from which the finished HTML is served.
  196. #html_use_opensearch = ''
  198. # This is the file name suffix for HTML files (e.g. ".xhtml").
  199. #html_file_suffix = None
  201. # Language to be used for generating the HTML full-text search index.
  202. # Sphinx supports the following languages:
  203. # 'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja'
  204. # 'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr'
  205. #html_search_language = 'en'
  207. # A dictionary with options for the search language support, empty by default.
  208. # Now only 'ja' uses this config value
  209. #html_search_options = {'type': 'default'}
  211. # The name of a javascript file (relative to the configuration directory) that
  212. # implements a search results scorer. If empty, the default will be used.
  213. #html_search_scorer = 'scorer.js'
  215. # Output file base name for HTML help builder.
  216. htmlhelp_basename = 'pyStimdoc'
  218. # -- Options for LaTeX output ---------------------------------------------
  220. latex_elements = {
  221. # The paper size ('letterpaper' or 'a4paper').
  222. #'papersize': 'letterpaper',
  224. # The font size ('10pt', '11pt' or '12pt').
  225. #'pointsize': '10pt',
  227. # Additional stuff for the LaTeX preamble.
  228. #'preamble': '',
  230. # Latex figure (float) alignment
  231. #'figure_align': 'htbp',
  232. }
  234. # Grouping the document tree into LaTeX files. List of tuples
  235. # (source start file, target name, title,
  236. # author, documentclass [howto, manual, or own class]).
  237. latex_documents = [
  238. (master_doc, 'pyStim.tex', u'pyStim Documentation',
  239. u'Alexander Tomlinson', 'manual'),
  240. ]
  242. # The name of an image file (relative to this directory) to place at the top of
  243. # the title page.
  244. #latex_logo = None
  246. # For "manual" documents, if this is true, then toplevel headings are parts,
  247. # not chapters.
  248. #latex_use_parts = False
  250. # If true, show page references after internal links.
  251. #latex_show_pagerefs = False
  253. # If true, show URL addresses after external links.
  254. # latex_show_urls = True
  256. # Documents to append as an appendix to all manuals.
  257. #latex_appendices = []
  259. # If false, no module index is generated.
  260. #latex_domain_indices = True
  263. # -- Options for manual page output ---------------------------------------
  265. # One entry per manual page. List of tuples
  266. # (source start file, name, description, authors, manual section).
  267. man_pages = [
  268. (master_doc, 'pyStim', u'pyStim Documentation',
  269. [author], 1)
  270. ]
  272. # If true, show URL addresses after external links.
  273. #man_show_urls = False
  276. # -- Options for Texinfo output -------------------------------------------
  278. # Grouping the document tree into Texinfo files. List of tuples
  279. # (source start file, target name, title, author,
  280. # dir menu entry, description, category)
  281. texinfo_documents = [
  282. (master_doc, 'pyStim', u'pyStim Documentation',
  283. author, 'pyStim', 'Software to generate visual stimuli for use in visual neuroscience experiments.',
  284. 'Miscellaneous'),
  285. ]
  287. # Documents to append as an appendix to all manuals.
  288. #texinfo_appendices = []
  290. # If false, no module index is generated.
  291. #texinfo_domain_indices = True
  293. # How to display URL addresses: 'footnote', 'no', or 'inline'.
  294. #texinfo_show_urls = 'footnote'
  296. # If true, do not generate a @detailmenu in the "Top" node's menu.
  297. #texinfo_no_detailmenu = False
  300. # Example configuration for intersphinx: refer to the Python standard library.
  301. intersphinx_mapping = {'https://docs.python.org/': None}
  304. # -----------------
  306. autodoc_member_order = 'bysource'
  308. # -- Options for PDF output --------------------------------------------------
  309. # Grouping the document tree into PDF files. List of tuples
  310. # (source start file, target name, title, author, options).
  311. #
  312. # If there is more than one author, separate them with \\.
  313. # For example: r'Guido van Rossum\\Fred L. Drake, Jr., editor'
  314. #
  315. # The options element is a dictionary that lets you override
  316. # this config per-document.
  317. # For example,
  318. # ('index', u'MyProject', u'My Project', u'Author Name',
  319. # dict(pdf_compressed = True))
  320. # would mean that specific document would be compressed
  321. # regardless of the global pdf_compressed setting.
  322. pdf_documents = [
  323. ('index', u'MyProject', u'pyStim', u'Alexander Tomlinson'),
  324. ]
  325. # A comma-separated list of custom stylesheets. Example:
  326. pdf_stylesheets = ['sphinx', 'kerning', 'a4']
  328. # A list of folders to search for stylesheets. Example:
  329. pdf_style_path = ['.', '_styles']
  331. # Create a compressed PDF
  332. # Use True/False or 1/0
  333. # Example: compressed=True
  334. #pdf_compressed = False
  336. # A colon-separated list of folders to search for fonts. Example:
  337. # pdf_font_path = [r'C:\Windows\Fonts']
  339. # Language to be used for hyphenation support
  340. #pdf_language = "en_US"
  342. # Mode for literal blocks wider than the frame. Can be
  343. # overflow, shrink or truncate
  344. #pdf_fit_mode = "shrink"
  346. # Section level that forces a break page.
  347. # For example: 1 means top-level sections start in a new page
  348. # 0 means disabled
  349. #pdf_break_level = 0
  351. # When a section starts in a new page, force it to be 'even', 'odd',
  352. # or just use 'any'
  353. #pdf_breakside = 'any'
  355. # Insert footnotes where they are defined instead of
  356. # at the end.
  357. #pdf_inline_footnotes = True
  359. # verbosity level. 0 1 or 2
  360. pdf_verbosity = 1
  362. # If false, no index is generated.
  363. pdf_use_index = False
  365. # If false, no modindex is generated.
  366. #pdf_use_modindex = True
  368. # If false, no coverpage is generated.
  369. #pdf_use_coverpage = True
  371. # Name of the cover page template to use
  372. #pdf_cover_template = 'sphinxcover.tmpl'
  374. # Documents to append as an appendix to all manuals.
  375. #pdf_appendices = []
  377. # Enable experimental feature to split table cells. Use it
  378. # if you get "DelayedTable too big" errors
  379. #pdf_splittables = False
  381. # Set the default DPI for images
  382. #pdf_default_dpi = 72
  384. # Enable rst2pdf extension modules (default is only vectorpdf)
  385. # you need vectorpdf if you want to use sphinx's graphviz support
  386. #pdf_extensions = ['vectorpdf']
  388. # Page template name for "regular" pages
  389. #pdf_page_template = 'cutePage'
  391. # Show Table Of Contents at the beginning?
  392. #pdf_use_toc = True
  394. # How many levels deep should the table of contents be?
  395. pdf_toc_depth = 2
  397. # Add section number to section references
  398. pdf_use_numbered_links = False
  400. # Background images fitting mode
  401. pdf_fit_background_mode = 'scale'

conf.py at commit 217add1, under GPL-3.0 · at the source

Overview

Authors: Teva W Bracha1, Nina Luong1, Joseph Leffler2, Benjamin Sivyer2, Kevin M Wright3
ORCID iDs: Nina Luong, Joseph Leffler, Benjamin Sivyer, Kevin M Wright
  1. Neuroscience Graduate Program, Oregon Health & Science University, Portland, OR 97239, USA
  2. Casey Eye Institute, Oregon Health & Science University, Portland, OR 97239, USA
  3. Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
Institutions: Oregon Health & Science University (United States); Vollum Institute (United States)
Journal: Development (Cambridge, England), volume 153, issue 9, article dev204980
Dates: received 28 May 2025; accepted 5 April 2026; published online 7 May 2026; in print May 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1242/dev.204980 · PMID 41968902 · PMCID PMC13200731 · OpenAlex W4410244644
Open access: hybrid, a free copy (OpenAlex)
Preprint: doi:10.1101/2025.05.08.652956
Status: code verified
Categories: mouse (organism)
Methods: Statistics, Evoked potentials, fMRI & imaging, Single-unit activity, calcium imaging
Keywords: Neuron, Retina, Dendrite, PTEN, Morphology
MeSH: Amacrine Cells*, Dendrites*, PTEN Phosphohydrolase*, Animals, Mice, Mice, Knockout, Neurodevelopment, Retina, Signal Transduction, TOR Serine-Threonine Kinases (* major topic)
Topic: Retinal Development and Disorders (Molecular Biology, Biochemistry, Genetics and Molecular Biology), according to OpenAlex
Funding: NINDS NIH HHS (T32NS007466); National Eye Institute (T32EY023211, R01EY032057, R01EY032564); NEI NIH HHS (T32EY023211, T32NS007466, R01EY032564, R01EY032057); National Institute of Neurological Disorders and Stroke (T32NS007466)
Citations: cited by 1 paper (Europe PMC); 85 references in the paper

Abstract

Neurons are subject to extensive developmental regulation to ensure precise subtype-specific morphologies that are intimately tied to their function. Starburst amacrine cells (SACs) in the mammalian retina have a highly stereotyped, radially symmetric dendritic arbor that is essential for their role in direction-selective circuits in the retina. We show that PTEN, the primary negative regulator of the PI3K-AKT-mTOR pathway that is highly implicated in neurodevelopmental disorders, regulates SAC morphology in a cell-autonomous manner. Pten-deficient mouse SACs show a nearly twofold increase in the number of dendritic branches, while other morphological properties remain largely unchanged. These morphological changes arise late in SAC development, after dendrite development is largely complete, and persist into adulthood. Mechanistically, excessive dendritic branching appears to arise from dysregulated mTOR activity. Despite this increase in dendritic branches, Pten-deficient SACs maintain a normal population number, normal organization of synaptic outputs and intact direction-selectivity in the retina. Collectively, these results show that PTEN is essential in mouse for the normal development of highly stereotyped neuronal morphology.

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

Repository

Its files are read in the Code ↔ Paper reader above.

SivyerLab/pystim

License: GPL-3.0
State: the link answers, verified on 28 September 2026
Evidence: files inventoried
Commit: 217add12282ca7419455ba347a64d4ab7a2030f0, 4 April 2023
Languages: Python (5)
Size: 43 files, 5 scripts
Software Heritage: not archived
Found in: the text, “Multi-electrode array recordings”
Holds: README, license file, environment (environment.yml, requirements-dev.txt, requirements.txt), tests, documentation
Not found: CITATION.cff, continuous integration
Tools: NumPy (3 files), PsychoPy (3 files), Pillow (2 files), SciPy (2 files), Matplotlib (1 file)
Availability: 1 check, the latest on 28 September 2026: the link answers
  • 28 September 2026: the link answers
7 files
At the source: github.com/SivyerLab/pystim

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;
  • 5 scripts, each with its path and the digest of its content;
  • no match between paragraphs and code yet;
  • 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 2, 28 September 2026

  • Publisher: — → The Company of Biologists
  • Authors: added Joseph Leffler (0000-0002-2751-0727); Benjamin Sivyer (0000-0002-4537-5768); removed Joseph Leffler; Benjamin Sivyer

Version 1, 28 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 5 authors, 5 keywords, 10 MeSH terms, 4 funders, 85 references.

Cite

This paper

Bracha, T. W., Luong, N., Leffler, J., Sivyer, B., & Wright, K. M. (2026). PTEN regulates starburst amacrine cell dendrite morphology during development. Development (Cambridge, England), 153(9), dev204980. https://doi.org/10.1242/dev.204980

BibTeX

@article{bracha2026pten,
author = {Bracha, Teva W and Luong, Nina and Leffler, Joseph and Sivyer, Benjamin and Wright, Kevin M},
title = {{PTEN regulates starburst amacrine cell dendrite morphology during development}},
journal = {Development (Cambridge, England)},
year = {2026},
month = may,
volume = {153},
number = {9},
pages = {dev204980},
publisher = {The Company of Biologists},
issn = {0950-1991},
doi = {10.1242/dev.204980},
url = {https://doi.org/10.1242/dev.204980},
pmid = {41968902},
pmcid = {PMC13200731}
}

RIS

TY - JOUR
AU - Bracha, Teva W
AU - Luong, Nina
AU - Leffler, Joseph
AU - Sivyer, Benjamin
AU - Wright, Kevin M
TI - PTEN regulates starburst amacrine cell dendrite morphology during development
T2 - Development (Cambridge, England)
J2 - Development
PY - 2026
DA - 2026/05/07
VL - 153
IS - 9
SP - dev204980
SN - 0950-1991
PB - The Company of Biologists
DO - 10.1242/dev.204980
UR - https://doi.org/10.1242/dev.204980
LA - en
ER -

CSL-JSON

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"PMCID": "PMC13200731",
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The tracing map gets a citation of its own once an author has validated it and it has a DOI.

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