spacetx/starfish

Issues

• Update numpy in REQUIREMENTS.txt for compatibility with Python 3.12

  #2024 opened 3 months ago by shachafl
  0

• 2d radius calculation in blob detection (blob.py) is incorrect

  #2022 opened 3 months ago by shachafl
  0

• Upgrading jsonschema to 4.18+ to resolve security issues with older dependencies breaks starfish

  #2020 opened 4 months ago by shachafl
  3

• Update scikit-image version (to >0.21) in REQUIREMENTS.txt file

  #2026 opened 3 months ago by shachafl
  0

• versioneeer.py breaks on installation

  #2011 opened 10 months ago by johnfmarkham
  4

• How can I do 3D spot detection or 3D decoding?

  #2010 opened 3 months ago by hziyin
  2

• Update installation section in the README.rst and readthedocs.io

  #2002 opened 3 months ago by shachafl
  1

• Unable to run dev install on Mac M2

  #2004 opened 4 months ago by ctcisar
  2

• Error in loading ISS data in quick start tutorial

  #2013 opened 4 months ago by rocketeer1998
  3

• Sphinx html latest build issues with missing top left icon and dropdown menu not working

  #2019 opened 4 months ago by shachafl
  0

• ValueError when running BlobDetector

  #2003 opened 2 years ago by iimog
  2

• question about quick start_display

  #2012 opened 10 months ago by YichengShao11
  2

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

  #1866 opened 5 years ago by mattcai
  1

• MinDistanceLabel does not enforce minimum distance, leading to over-segmentation

  #2006 opened a year ago by iimog
  1

• Couldn't install without specifying an older version of scikit-image (0.17.2)

  #1988 opened 2 years ago by ryandikdan
  5

• barcodeBuildFunc modifies external variables

  #2007 opened a year ago by guoyang-github
  1

• Possible parameter inversion in LearnTransform.Translation class

  #2005 opened a year ago by guoyang-github
  2

• blob throws error when run with no `reference_image` and `is_volume=False`

  #1870 opened 5 years ago by mattcai
  2

• Link to raw data is not working

  #1937 opened 4 years ago by mstemmer
  2

• AttributeError: 'DataArray' object has no attribute 'flags' in quick start run

  #1952 opened 3 years ago by sebherbert
  9

• starfish is incompatible with Python 3.9

  #1950 opened 3 years ago by ora-lv
  1

• Tutorials making use of Napari should include screenshots of expected output.

  #1925 opened 4 years ago by vals
  1

• JOSS paper should mention how starfish compares to the other available tools

  #1927 opened 4 years ago by vals
  0

• Are the masks in the left in the tutorial really two cells?

  #1926 opened 4 years ago by vals
  2

• error importing scikit's 'match_histograms'

  #1932 opened 4 years ago by juliomateoslangerak
  2

• 'Visualizing Data' tutorial crashes at viewer.add_image step

  #1924 opened 4 years ago by vals
  3

• make install-dev got error

  #1922 opened 4 years ago by giovp
  0

• JOSS paper does not mention alternative tools

  #1905 opened 4 years ago by vals
  0

• JOSS MS comments

  #1907 opened 4 years ago by shazanfar
  1

• Displaying example from data formatting tutorial

  #1903 opened 4 years ago by vals
  3

• Include output in example notebooks

  #1904 opened 4 years ago by vals
  2

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

  #1912 opened 4 years ago by aschrader5
  0

• Update open napari window?

  #1902 opened 4 years ago by vals
  1

• Quickstart and napari

  #1901 opened 4 years ago by vals
  2

• More intuitive ordering for the link to documentation

  #1900 opened 4 years ago by vals
  1

• Tutorial "Loading ImageJ ROI Sets"

  #1899 opened 4 years ago by giovp
  2

• IlastikPretrainedProbability is not compatible with cropped ImageStack

  #1867 opened 5 years ago by mattcai
  0

• Tutorial "Pre-defined Watershed Segmentation Pipeline"

  #1898 opened 4 years ago by giovp
  0

• Tutorials "How to normalize" improvements.

  #1897 opened 4 years ago by giovp
  2

• Tutorial "Showing Image of ImageStack Plane" does not run

  #1896 opened 4 years ago by giovp
  3

• register_translation is deprecated

  #1887 opened 5 years ago by lambdamoses
  2

• readthedocs fails to build because 'DataArray' object has no attribute 'flags'

  #1885 opened 5 years ago by mattcai
  0

• duplicate spot_ids returned when using build_traces_sequential

  #1871 opened 5 years ago by mattcai
  1

• add image banner to landing page

  #1859 opened 5 years ago by neuromusic
  0

• get sphinx-gallery to render all examples

  #1865 opened 5 years ago by neuromusic
  0

• hide code blocks in examples

  #1864 opened 5 years ago by neuromusic
  0

• suppress progress bar output in doc examples

  #1863 opened 5 years ago by neuromusic
  0

• add traffic analytics to docs

  #1862 opened 5 years ago by neuromusic
  0

• make sure readthedocs ad banner doesn't block content

  #1861 opened 5 years ago by neuromusic
  0

• suppress all warnings in docs

  #1860 opened 5 years ago by neuromusic
  0