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TiffCropper v1.2

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@Juaco2r Juaco2r released this 20 May 21:15
· 25 commits to main since this release
v1.2
2899724

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

TiffCropper supports high-resolution ROI extraction, fixed-size tile generation, row/column-based image division, and tile merging workflows for Whole Slide Images (WSI) and large microscopy files.

DOI: 10.5281/zenodo.20316535

Highlights

  • Support for TIFF, pyramidal TIFF, OME-TIFF, SVS, NDPI, MRXS, JPEG, and PNG
  • ROI cropping with exact pixel-coordinate control
  • Interactive crop rectangle selection from the image preview
  • Full-image area selection for whole-slide export or downsampling
  • Fixed-size square tile generation with optional overlap
  • Row/column-based image division for structured tiling
  • Bulk tiling of multiple images using the same parameters
  • Automatic tile merging from encoded tile names
  • Manual grid-based tile merging when filenames do not encode position
  • OME-TIFF export with physical pixel size preservation when available
  • Correct scaling of physical pixel size metadata after downsampling
  • Calibration metadata reuse during merge when available
  • Optional lossless DEFLATE compression
  • BigTIFF output for large crops, tiles, and merged images
  • Pyramid-aware preview for large images
  • Robust OpenSlide fallback strategy for partially corrupted pyramid blocks
  • Memory-safer external padding crop during merge
  • Batch tiling CSV logs
  • Help/About dialog with citation, DOI, supported formats, and usage notes
  • Windows executable designed to run without a separate Python installation

Designed for Digital Pathology Workflows

TiffCropper enables precise pixel-level cropping, tiling, and reconstruction while preserving relevant calibration metadata when available.

The application can preserve or propagate:

  • Resolution metadata, such as DPI
  • Physical pixel size, such as µm per pixel
  • OME-TIFF physical size metadata
  • OpenSlide scanner metadata, embedded as OME MapAnnotations when exporting OME-TIFF
  • Tile coordinate information in output filenames

When crops or tiles are downsampled, TiffCropper updates the physical pixel size accordingly. For example, if the original image has a pixel size of 0.25 µm/px and the output is saved with downsample 2, the resulting pixel size is written as 0.50 µm/px.

Tiling and Merge Improvements

TiffCropper v1.2 supports two tiling strategies.

Fixed square tiles

The image is divided into square tiles of a user-defined size. Optional overlap can be applied between neighboring tiles.

Padding is applied only to true border tiles. Internal tiles are extracted as direct crops to avoid introducing artificial black or white padding inside the image.

Divide image by rows/columns

The image can also be divided into a user-defined number of rows and columns. This mode may generate rectangular tiles and does not add artificial padding.

Tile names include row, column, division grid size, and original pixel coordinates to support traceability and reconstruction.

Merge mode

Merge mode can reconstruct tiled images using either automatic filename parsing or manual grid assignment.

The merge operation is geometric. It does not perform image registration or intelligent stitching. For best results, merge tiles generated from the same source image using the same tile size, overlap, and downsample settings.

Included in this Release

  • TiffCropper-Windows.zip → Windows executable package
  • TiffCropper-Linux.tar.gz → Linux artifact
  • 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
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