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Releases
v1.7.4
v1.7.3
- pypi package
Full Changelog: v1.7.2...v1.7.3
v1.7.2
v1.7.1
- Microscope Type SP5 -> Confocal
Full Changelog: v1.7.0...v1.7.1
v1.7.0
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Added support for legacy Leica SP5/LAS AF files using MemoryBlockID fallback identifiers.
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Fixed nested folder and image discovery for LIF, XLEF and LOF containers.
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Added extract_nested_leica_items() to list all image IDs in a Leica file.
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Improved SP5 metadata extraction, including microscope, objective, lasers, wavelengths, detectors and scan settings.
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Corrected negative Z-spacing and spatial-unit handling in time-series metadata.
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Improved OME-TIFF/OME-Zarr metadata for objectives, excitation and emission wavelengths.
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Added microscope, objective and wavelength details to the Qt metadata display.
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Added regression tests using real and synthetic legacy SP5 data.
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Also included changes made by P.K. for list of all userIDs
Full Changelog: v1.6.0...v1.7.0
v1.6.0
- bug fixes
- added convert to OME-Zarr
Full Changelog: v1.5.0...v1.6.0
v1.5.0
v1.4.1
- significant bits now used to calculate white and black levels
Full Changelog: v1.4.0...v1.4.1
v1.4.0
🚀 Robust Network File Operations
This release focuses on reliability when working with files on network drives and large datasets.
✨ New Features
Robust File Reading (Temp-First Approach)
- Source file copying: Before processing, source files are now copied to a local temp folder to prevent network interruptions from corrupting reads
- Progress bar for source copying: Visual feedback while copying large source files from network locations
- Automatic cleanup: Temp source files are cleaned up after processing completes
Robust File Writing (Temp-First Approach)
- Safe TIFF saving: OME-TIFF files are first written to local temp storage, then copied to the destination with verification
- Retry logic: Up to 10 retry attempts with progressive backoff (1 min, 2 min, ... up to 10 min) for network copy failures
- Size verification: Each copy is verified by comparing file sizes before cleanup
Enhanced Progress Indicators
- Aligned progress bars: All progress bars are now visually aligned for clean, readable output
- Distinct visual styles for different operations
- Elapsed time tracking: Each progress bar shows elapsed time upon completion
[Xm Ys] - Total time display: Shows cumulative processing time at the end
LIF Extraction Improvements
- Block-level retry: When extracting images from LIF files, each 25MB block can be retried independently on read errors
📦 Requirements Reorganization
Split requirements into scenario-specific files:
- requirements-docker.txt — Core dependencies for Docker/CLI
- requirements-server.txt — For web server
- requirements-qt6ui.txt — For Qt6 desktop GUIs (includes PyQt6)
📋 Example Output
Copying source: {▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒} 100.0% - 65/65 MB [2.1s]
Converting to OME-TIFF: |████████████████████████████████████████| 100.0% Processing complete [0.2s]
Saving: <▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓▓> 100.0% - Writing TIFF [1.2s]
Copying output: {▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒} 100.0% - 46/46 MB [1.7s]
Copying alt output: {▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒} 100.0% - 46/46 MB [1.7s]
Total time: 7.4s
Cleaned up temp output file
Cleaned up temp source file
🐛 Bug Fixes
- Fixed progress bar overwriting issues when transitioning between phases
- Fixed duplicate 100% progress lines from pyvips callbacks
- Ensured proper line clearing with minimum suffix width padding
📚 Documentation Updates
- Updated README.md with new requirements structure
- Updated Dockerfile to use requirements-docker.txt
- Updated ConvertLeicaQT.md and Server.md with robust file handling notes
Full Changelog: v1.3.1...v1.4.0