Reads Standard BioTools .mcd files and writes OME-TIFFs for QuPath, Napari and Fiji.
- Convert — each region (ROI) becomes its own multi-channel OME-TIFF.
- Stitch — all regions onto one canvas, placed by recorded stage coordinates.
- Post-process — channel subsets, pyramidal copies, re-compression.
🚀 Quick start
Requires Python 3.9+. Runs on Windows, macOS and Linux.
pip install mcd_stitcher
Convert each region to its own OME-TIFF:
mcd_process "path/to/file.mcd" --convert
Stitch all regions into a single image:
mcd_process "path/to/file.mcd" --stitch --pyramid
💡 Tip —
--pyramidadds tiled, multi-resolution copies that let large stitched files pan and zoom smoothly, especially on low-RAM systems.
Everything lands in MCD_Processed/<file name>/, next to your input.
🔬 What it does
Left: Ten regions from one .mcd file, shown to common scale. Right: the same ten placed on a single 7.0 × 4.6 mm canvas at 0.5 µm/px.
--convert writes each region to its own OME-TIFF and --stitch places them all on one canvas using the stage positions recorded in the file — no registration, no seam blending. Regions acquired at different step sizes are resampled onto the finest common grid.
Native resolution is preserved end to end
A 7.0 × 4.6 mm canvas at 0.5 µm/px still resolves single cells — stitching costs no detail. --pyramid adds the tiled copy that makes a canvas this size navigable.
⚡ Commands
mcd_process <input_path> [<output_path>] [OPTIONS] # a .mcd file, or a folder of them
mcd_process "file.mcd" -m # inspect: regions, panoramas, channel indices
mcd_process "file.mcd" --convert # one OME-TIFF per region
mcd_process "file.mcd" --stitch --pyramid # one zoomable stitched canvas
mcd_process "folder/" --convert --stitch # a whole batch, both outputs, single pass
🔧 All options, output layout and the Python API
| Option | What it does |
|---|---|
--convert |
One OME-TIFF per region. |
--stitch |
All regions onto one canvas. |
-p, --panorama |
Panorama overviews; large ones get region outlines. |
-m, --metadata |
Print regions, panoramas, indexed channels. Writes nothing. |
--roi_map IDX |
Region → panorama pixel map. Needs convert/stitch. |
-f, --filter "LIST" |
Keep only these channels, e.g. "0-5,7". Indices from -m. |
--pyramid |
Also write a tiled, multi-resolution copy. |
-r, --roi "LIST" |
Only these regions, e.g. "0-5,7". Indices from -m. |
-d, --output_type |
uint16 (default) / float32. |
-c, --compression |
zstd (default) / LZW / None. |
--max-memory SIZE |
Cap memory for image buffers, e.g. 8G. Detected automatically from the container/scheduler limit or free RAM; set this to override, or on a shared machine where you want a reproducible plan. Also read from $MCD_STITCHER_MAX_MEM. |
-f and --pyramid are post-processing steps and need --convert or --stitch.
MCD_Processed/<file name>/
├── <region>.ome.tiff --convert
├── <file name>_stitched.ome.tiff --stitch
├── <file name>_slide_0_pano_0.png -p (+ _overlay.png)
└── <file name>_slide_0_pano_0_roi_map.txt --roi_map
mcd_convert, mcd_stitch and tiff_subset each do one step; tiff_subset works on existing OME-TIFFs.
from mcd_stitcher import mcd_process
mcd_process(input_path="file.mcd", convert=True, stitch=True)
📄 Citation
Chaurasia, P. (2026). MCD Stitcher: An open-source tool for whole-slide stitching and conversion of Imaging Mass Cytometry data. bioRxiv. https://doi.org/10.64898/2026.06.26.732348
BibTeX
@article{chaurasia2026mcdstitcher,
title = {MCD Stitcher: An open-source tool for whole-slide stitching and conversion of Imaging Mass Cytometry data},
author = {Chaurasia, Pawan},
journal = {bioRxiv},
year = {2026},
doi = {10.64898/2026.06.26.732348}
}
📜 License, issues & changelog
MIT — see LICENSE. Report problems on the issue tracker; release notes are in the changelog.
1 maintainer
Metadata
1 maintainer
Release files for mcd-stitcher 2.4.0
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