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Scripts and dependencies updates for Python 3.8 - 3.10

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The motivation for this PR was significant algo improvements for blob detection in scikit-image 0.20 released on February 2023, together with some recommendations for the python scientific community about maintaining...

Curtesy request for the public - Please update the installation section in README.rst and readthedocs.io to clone the repo and pip install in development mode (pip install -e .). The...

Hi, I have followed the documentation on installing Julia (ver 1.7.2) on Linux (Ubuntu), and added the Julia packages as well as the "IJulia" package to allow Julia kernel on...

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

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#### Description To resolve a few security issues with older dependencies, I wish to upgrade jsonschema to 4.18+, but this breaks starfish and throws errors in testing as RefResolver was...

Scikit-image is pinned to version 0.21 as newer versions modified some modules and this needs to be updated in starfish so imports will work. Also need to replace "selem" (deprecated...

#### Description Sphinx html latest build has two issues: 1) Missing top left icon (html_logo) 2) "More" dropdown menu not working on the top navigation bar Probably an issue with...

fix: index shift correction for blob detection in 2d tiles

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This closes #2075 & #1870 There might be another solution to this as I couldn't figure why when running blob detection with `is_volume=False` and with a reference image gives a...

#### Description Issue discovered by [Leo Juhlin](https://forum.image.sc/t/tutorial-with-blobdetector-yields-incorrect-results/112432/4) when running the example code for [howto-spotfindingresults]( https://spacetx-starfish.readthedocs.io/en/latest/gallery/how_to/assess_spotfindingresults.html#howto-spotfindingresults) "y-values of detected spots, shown in y-column all being 0, and the radius of the...

Drop Python 3.9 support due to critical security issue with a dependency

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We have kept support for Python 3.9 beyond its recommended life span although it was dropped by the scientific community in April 2024 (https://numpy.org/neps/nep-0029-deprecation_policy.html). A critical vulnerability in Dask

We have kept support for Python 3.9 beyond its recommended life span although it was dropped by the scientific community in April 2024 (https://numpy.org/neps/nep-0029-deprecation_policy.html). A critical vulnerability in Dask