Fogg Lab Tissue Model Analysis Tools

What's Changed

• Save another intermediate output in compute_branches.py by @wigginno in #76
• fix loading z stacks from image sequences by @wigginno in #77
• Fix bugs related to image loading and saving by @wigginno in #78
• Clean up output messages and filenames by @wigginno in #80
• Reduce mem usage. Improve logs & output filenames by @wigginno in #81
• Improve input directory validation by @wigginno in #82

Full Changelog: https://github.com/fogg-lab/tissue-model-analysis-tools/commits/v1.0.6

Fogg Lab Tissue Model Analysis Tools

GUI! (and other updates)

This release includes the graphical user interface, a portable and standalone program that runs without installation on Windows, Linux, and macOS. The macOS build will be added to this release soon.

Screenshot of the GUI Program

Fogg Lab Tissue Model Analysis Tools

What's Changed

• Distribute command-line application using pipx by @wigginno in #58

Full Changelog: v1.0.3...v1.0.4

Fogg Lab Tissue Model Analysis Tools

What's Changed

• General improvements by @wigginno in #50
• Fix zproj script for using OME-TIFF files by @wigginno in #52
• Image intensity rescaling by @wigginno in #53
• Add vessel_probability_thresh config param to branching script by @wigginno in #54
• Make weights files compatible with TF 2.13.1 by @wigginno in #55
• Specify out_range for intensity rescaling in data_prep.py by @wigginno in #56

Full Changelog: v1.0.2...v1.0.3

Fogg Lab Tissue Model Analysis Tools

What's Changed

• Replace MIT with academic research license by @wigginno in #49

Full Changelog: v1.0.1...v1.0.2

v1.0.1

What's Changed

• Create more durable conda environment files by @wigginno in #46
• Update Conda environment file for Windows by @wigginno in #47
• Maintenance on the Colab notebooks

Full Changelog: v1.0.0...v1.0.1

v1.0.0

• Update well masking so it works for square wells

v1.0.0-beta

Major changes:

• Updated the binary segmentation training notebook
• Added a standalone analysis demo notebook, and removed individual analysis notebooks
• Created the data repo and added a function to download example input images from it
• Add platform-specific conda environment files with pinned versions for better reproducibility

Full Changelog: v1.0.0-alpha...v1.0.0-beta

v1.0.0-alpha

• #24 The notebooks are out of date
• #26 environment.yml does not include versions for the dependencies