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TiffCropper v1.3

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@Juaco2r Juaco2r released this 02 Jul 15:06
· 5 commits to main since this release
v1.3
3308ae8

Stable public release of TiffCropper, a standalone application for cropping, tiling, previewing, and reconstructing large digital pathology and microscopy images.

TiffCropper supports high-resolution ROI extraction, fixed-size tile generation, row/column image division, tile merging workflows, pyramid-aware previews, and basic IF threshold exploration.

DOI

Highlights

  • Support for TIFF, pyramidal TIFF, OME-TIFF, SVS, NDPI, MRXS, JPEG, and PNG
  • ROI cropping with exact pixel-coordinate control
  • Interactive crop selection from image preview
  • Full-image export and downsampling options
  • Fixed-size tile generation with optional overlap
  • Row/column-based image division
  • Bulk tiling for multiple images
  • Automatic and manual tile merging
  • BigTIFF output for large crops, tiles, and merged images
  • OME-TIFF export with physical pixel size preservation when available
  • Correct physical pixel size scaling after downsampling
  • Improved calibration preservation for OME-TIFF and IF crops
  • Pyramid-aware preview for large images
  • Safer handling of very large crop regions
  • Improved RGB/Samples-axis TIFF handling during crop export
  • Memory-safer merge and padding operations
  • Optional lossless DEFLATE compression
  • Batch tiling CSV logs
  • New IF Cell / Tissue Threshold Explorer
  • Fast IF threshold visualization using QuPath measurements CSV files
  • Lightweight SQLite cache for large GeoJSON cell overlays
  • Overlay toggle for quick comparison with the raw image
  • More compact interface for Linux and smaller screens
  • Help/About dialog with citation, DOI, supported formats, and usage notes
  • Windows executable designed to run without a separate Python installation

IF Threshold Explorer

Version 1.3 introduces an experimental IF threshold exploration mode for fluorescence microscopy workflows.

The module can use:

  • A multichannel IF image, such as OME-TIFF
  • A cell GeoJSON file
  • An optional QuPath measurements CSV file

When a QuPath CSV is provided, TiffCropper can use existing cell-level measurements such as:

Cell: FAP (C2): Mean
Cell: aSMA (C3): Mean
Cell: Cancer (C4): Mean

This allows fast visual testing of positivity thresholds without recalculating intensities from the image.

Crop and Preview Improvements

Version 1.3 improves crop preview and export behavior for very large images.

The preview system now attempts to use available pyramid or overview levels before falling back to full-resolution access. This improves responsiveness for large TIFF, pyramidal TIFF, and OME-TIFF images.

Crop export was also updated to better preserve calibration metadata and avoid unsafe memory allocation for very large regions.

Tiling and Merge

TiffCropper supports two tiling strategies:

  1. Fixed square tiles with optional overlap.
  2. Row/column division for structured rectangular tiling.

Merge mode can reconstruct tiled images using encoded filenames or manual grid assignment.

The merge operation is geometric and does not perform image registration or intelligent stitching.

Included in this Release

  • TiffCropper-Windows.zip → Windows executable package
  • TiffCropper-Linux.tar.gz → Linux artifact, when generated successfully
  • TiffCropper-macOS.zip → macOS artifact, when generated successfully
  • Source code
  • README.md
  • LICENSE
  • CITATION.cff
  • requirements.txt
  • THIRD_PARTY_NOTICES.md, when included

No installation is required for the Windows executable.

Simply extract the package and run:

TiffCropper.exe

Notes

  • Raw IF crops and tiles are saved without intensity normalization.
  • Using a QuPath measurements CSV is recommended for faster IF threshold exploration.
  • Existing crops generated with older versions may need to be regenerated if calibration metadata was not preserved correctly.
  • The merge operation does not perform image registration.
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