mcd-stitcher 2.5.0

Reads Standard BioTools .mcd files and writes OME-TIFFs for QuPath, Napari and Fiji — from a desktop app, the command line or Python.

• 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

Then open the desktop app:

mcd_gui

Choose a .mcd file — or switch to Batch for a folder of them — tick the outputs you want and press Run. Everything lands in MCD_Processed/<file name>/, next to your input.

💡 Tip — tick Pyramid as well. It adds tiled, multi-resolution copies that let large stitched files pan and zoom smoothly, especially on low-RAM systems.

Prefer the command line or Python? The command-line guide and the Python API are in the documentation, along with tutorials and troubleshooting:

🔬 How it works

_{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.}

1. Read — each region comes straight out of the .mcd file with its channels, pixel size and stage position.
2. Convert — every region is written to its own OME-TIFF, channel names included.
3. Stitch — the regions are placed on one canvas at their recorded stage positions: no registration, no seam blending. Regions acquired at different step sizes are resampled onto the finest common grid, and where regions overlap the earliest acquisition stays on top.
4. Post-process — optional channel subsets and pyramidal copies, made from the files above.

Large slides are processed in pieces sized to the memory available, so the same run works on a laptop and on a cluster node.

⚡ Commands

mcd_process "file.mcd" -m                     # inspect: regions, panoramas, channel indices
mcd_process "folder/" --convert --stitch      # every .mcd in a folder, both outputs
mcd_process "file.mcd" --stitch -r "0-3"      # stitch only regions 0–3 (indices from -m)
mcd_process "file.mcd" --convert -f "0-5,7"   # plus copies with only these channels

📖 Every option, the output layout and more examples are in the command-line guide.

📄 Citation

If MCD Stitcher helps your work, please cite:

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

@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}
}

🐛 Issues and questions

Found a bug or have a question? Open an issue on the issue tracker. A log helps: tick Save a log file in the app, or paste the command's output.

📝 Changelog

Release notes are in CHANGELOG.md, and on the documentation site.

📜 License

MIT — see LICENSE.