SenoQuant 1.0.0-beta11-post4

Highlights

• Fixed installation/launch problem associated with napari 0.7.0
• Visualization now works when more than one compatible data table exists under the same directory.

Known Issue

• SenNet portal is still not working. Cause narrowed down to a behavior change in the param-search API. Will implement the fix soon. #27

What's Changed

• Feature viz by @yeaehan in #25
• Select a single file for visualization input by @yeaehan in #26

Full Changelog: senoquant-v1.0.0-beta11-post3...senoquant-v1.0.0-beta11-post4

SenoQuant 1.0.0-beta11-post3

• Hardened installer cert handling. Updated uv to use the system trust store. Should allow installation on corporate networks.

Full Changelog: senoquant-v1.0.0-beta11...senoquant-v1.0.0-beta11-post3

SenoQuant 1.0.0-beta11

Highlights

• Unified sanitization scheme across saved files.
• Column merging in quantification and batch when there are >= 2 segmentations per Markers feature.
  • This only occurs when there is a strict 1:1 correspondence between the labels and tokens (sanitized names) of the segmentations.
  • New merged_wide file prefixes column names with nuclear_#_ / cyto_#_ (based on segmentation type), and the tokens and raw names per segmentation are saved as well.
• Updated visualization to accept merged_wide.

Full Changelog: senoquant-v1.0.0-beta10...senoquant-v1.0.0-beta11

SenoQuant 1.0.0-beta10

Highlights

• Faster ROI processing
• Morphological models now won't dilate into neighboring cells
• Faster saving with parallel morphological parameter calculations
• napari layer names now contain channel names in the image files, if available
• Auto-populate channel(s) buttons for Markers, Spots, and Batch
• Better visualization plots
• Fixed ROI processing in 3D #21
• Fixed RMP detector padding error #20

What's Changed

• Feature viz by @yeaehan in #22
• Fix unassigned cells to color grey by @yeaehan in #23

Full Changelog: senoquant-v1.0.0-beta9...senoquant-v1.0.0-beta10

SenoQuant 1.0.0-beta9

Highlights

• Added OME-ZARR support.
• Much faster readers.
• Better backend widget and thread cleanup.
• More consistent Batch behavior.
• Added a help button in the top-right corner that opens the current tab's User Guide page.

Please click on > Assets to access the installers.

Full Changelog: senoquant-v1.0.0-beta8-post2...senoquant-v1.0.0-beta9

SenoQuant 1.0.0-beta8-post2

Highlights

• Optimized morphological models.
• Improved SenNet Portal and Batch layouts

Please click on > Assets to access the installers.

Full Changelog: senoquant-v1.0.0-beta8-post1...senoquant-v1.0.0-beta8-post2

SenoQuant 1.0.0-beta8-post1

Highlights

• Fixed CLI discovery issue.

Please click on > Assets to access the installers.

Full Changelog: senoquant-v1.0.0-beta8...senoquant-v1.0.0-beta8-post1

SenoQuant 1.0.0-beta8

Highlights

• Added the SenNet Portal tab. Use it to discover and download compatible SenNet datasets.
• Added a shutdown manager to help clean up processes better.

Please click on > Assets to access the installers.

Full Changelog: senoquant-v1.0.0-beta7...senoquant-v1.0.0-beta8

SenoQuant 1.0.0-beta7

Highlights

• Added remote save/load paths support across tabs.
• Improved colocalization point visualization.
• Defaulted Batch process-all-scenes to checked.
• Console notifications now show up more reliably across UI tabs.
• Optimized marker and spots export.
• Optimized the RMP spot detector's settings.

Full Changelog: senoquant-v1.0.0-beta6-post5...senoquant-v1.0.0-beta7

Please click on > Assets to access the installers.

SenoQuant 1.0.0-beta6-post5

Highlights

• Fixed reader error for network paths (shared drives, etc.).

• Added cross-platform Java truststore setup for BioFormats bootstrap:

  • Windows: Windows-ROOT / SunMSCAPI
  • macOS: KeychainStore
  • Linux: system Java cacerts when available
  • Opt-out via SENOQUANT_JAVA_TRUSTSTORE_SETUP=off

Full Changelog: senoquant-v1.0.0-beta6...senoquant-v1.0.0-beta6-post5