Issues

• fix: repair broken AWS S3 links and add missing data links in osmFISH and ISS breast data-formatting examples

  bug
  spacetx/starfish#2216 · Filter by author shachafl opened on Apr 13, 2026

• mypy ver 1.11+ multiple errors

  bug
  spacetx/starfish#2205 · Filter by author shachafl opened on Mar 19, 2026

• missing notebooks to python scripts validation in Github Actions workflow

  bug
  spacetx/starfish#2201 · Filter by author shachafl opened on Mar 18, 2026
  

• Difference between SeqFISH.ipynb and SeqFISH.py raising an error in make fast

  bugdocs
  spacetx/starfish#2195 · Filter by author shachafl opened on Feb 26, 2026
  1

  

• Fix a FutureWarning depreciation for the plugin parameter in skimage.io

  bug
  spacetx/starfish#2191 · Filter by author shachafl opened on Feb 25, 2026
  

• Minor improvements in Makefile for new releases

  docs
  spacetx/starfish#2189 · Filter by author shachafl opened on Feb 25, 2026
  

• In some downloadable scripts from ReadTheDocs executable code is labeled as markdown and requires excessive manual edits

  docs
  spacetx/starfish#2161 · Filter by author shachafl opened on Nov 24, 2025

• seqFISH pipeline doesn't appear on ReadTheDocs pipeline examples

  bug
  spacetx/starfish#2153 · Filter by author shachafl opened on Nov 5, 2025

• napari tests failing

  bug
  spacetx/starfish#2069 · Filter by author iimog opened on May 9, 2025
  3

• Using return instead of assert in starfish/core/spots/FindSpots/test/test_spot_detection.py

  bug
  spacetx/starfish#2067 · Filter by author shachafl opened on May 6, 2025
  

• Missing test coverage for some scripts published on Starfish ReadTheDocs

  spacetx/starfish#2065 · Filter by author shachafl opened on Apr 16, 2025
  1

• barcodeBuildFunc modifies external variables

  bug
  spacetx/starfish#2007 · Filter by author guoyang-github opened on Nov 16, 2023
  1

• Possible parameter inversion in LearnTransform.Translation class

  bug
  spacetx/starfish#2005 · Filter by author guoyang-github opened on Nov 15, 2023
  2

• "ValueError: in1 and in2 should have the same dimensionality" when "is_volume=True" for Filter.DeconvolvePSF

  bug
  spacetx/starfish#1912 · Filter by author aschrader5 opened on Nov 4, 2020

• IlastikPretrainedProbability is not compatible with cropped ImageStack

  bug
  spacetx/starfish#1867 · Filter by author mattcai opened on Apr 10, 2020 · 0.4.x

• ApplyTransform.Warp.run() alters the TransformsList such that it can't be used again

  bug
  spacetx/starfish#1866 · Filter by author mattcai opened on Apr 10, 2020 · 0.4.x
  1

• get sphinx-gallery to render all examples

  docs
  spacetx/starfish#1865 · Filter by author neuromusic opened on Apr 10, 2020

• hide code blocks in examples

  docs
  spacetx/starfish#1864 · Filter by author neuromusic opened on Apr 10, 2020

• suppress progress bar output in doc examples

  docs
  spacetx/starfish#1863 · Filter by author neuromusic opened on Apr 10, 2020

• add traffic analytics to docs

  docs
  spacetx/starfish#1862 · Filter by author neuromusic opened on Apr 10, 2020

• make sure readthedocs ad banner doesn't block content

  docs
  spacetx/starfish#1861 · Filter by author neuromusic opened on Apr 10, 2020 · JOSS submission

• suppress all warnings in docs

  docs
  spacetx/starfish#1860 · Filter by author neuromusic opened on Apr 10, 2020 · JOSS submission

• add an ‘advanced analysis’ section with musings about things one might do

  docs
  spacetx/starfish#1858 · Filter by author neuromusic opened on Apr 10, 2020

• Correcting Images How to: deconvolution

  docs
  spacetx/starfish#1857 · Filter by author neuromusic opened on Apr 10, 2020

• Correcting Images How to: chromatic aberration

  docs
  spacetx/starfish#1856 · Filter by author neuromusic opened on Apr 10, 2020