Bell Jar v5.2.0-beta

Changelog

• Fixed bug causing counts to fail with new alignments
• Fixed bug with adjustments resulting in corrupted .pkl files
• Adjustments also now work with new alignments
• Registration method updated to include new initial affine transforms before the deformable step to increase the quality

Bell Jar v5.1.0-beta

Changelog

• Alignments now also save your optimal alignment to your tissue folder in a human-readable format
• Previous alignment values are reloaded each time you run the same tissue, provided the directory has not changed
• Saved values are based on file name so they will be agnostic to removing or adding in new tissue as experimental datasets evolve

Major Issues

• All older major versions (e.g. 4.x.x) produced annotations that are completely incompatible with future releases. Please only use v5.x.x moving forward

If you have any issues or requests please open an issue on Git Hub.

Bell Jar v5.0.0-beta

Change log

• Added a new method for handling separated tissue
• Fixed bug with intensity by region, causing it to get shifted values from annotations

Key

• This version produces files not backwards compatible with any prior versions

Bell Jar v4.1.0-beta

Changelog

• Added a new centering step to alignment to improve non-rigid transform performance
• Switched Demons algorithm to FastSymetricForces to achieve better performance
• Fixed bug causing warping to crash and spit out blank annotations

Key

• The alignment step should now be significantly faster (~5 minutes per section)

Please open an issue if you encounter any problems or have feature requests.

Bell Jar 4.0.1-beta

Changelog

• Fixed bug causing alignment to fail
• Reduced iterations in alignment to speedup process
• Included new affine step back into deformable step to increase accuracy

If you encounter any issues please open and issue here on Git Hub for the fastest response.

Bell Jar v3.5.1-beta

Changelog

• Major bug fix for TIFF images over 1GB, all routines now support large images
• Proper version number now displayed from package directly
• Intensity by region allows maps to be used to collect direct intensity data as ROIs instead of only cell counts

Please open an issue if you run into any problems.

Review Beta

An advanced version of Bell Jar for QA testing in preparation for developing our first release candidate. Includes improved adjustments, intensity by region, and many bug fixes/performance improvements.

Bell Jar Beta

Full Changelog: https://github.com/asoronow/belljar/commits/v3.0.0-beta

Fundamental features remained the same. Install now requires an internet connection and will download all the necessary files. The total install size is about 55GB. A major known issue with this release is the inability to support arm64-based devices due to some of the python dependencies lacking arm64 support. Future full releases will address this issue. Please report any other issues here on GitHub.

To install, extract the folder somewhere and run the executable. If you want, you may also build from source or run from source by using the provided yarn commands.