Getting started

Install

MCD Stitcher needs Python 3.9 or newer and runs on Windows, macOS and Linux.

pip install mcd_stitcher

Give it its own environment

A separate conda or virtual environment keeps its dependencies apart from your other tools:

conda create -n mcd python=3.12
conda activate mcd
pip install mcd_stitcher

On Linux the desktop app also needs Tk — see Troubleshooting if mcd_gui does not start.

Your first stitched image

Desktop appCommand line

1. Start the app:

   mcd_gui
   

2. Click Browse… next to File and choose a .mcd file. Its regions and channels fill the tables.

3. Under Outputs, tick Stitch and Pyramid.
4. Press Run. When it finishes, Open output folder shows the results.

mcd_process "path/to/file.mcd" --stitch --pyramid

Each step reports as it finishes:

Where the files go

Unless you choose a folder, everything lands in MCD_Processed/<file name>/, next to the .mcd file. To write somewhere else, use Save to in the app, or give a second path on the command line; each file then gets its own folder inside it:

mcd_process "path/to/file.mcd" "path/to/results" --stitch --pyramid

Open the result

File	What it is
<file name>_stitched.ome.tiff	The stitched canvas.
<file name>_stitched_pyramid.ome.tiff	The same canvas stored as tiles at several resolutions — the one to open for smooth panning and zooming.

Open it in any viewer that reads OME-TIFF. Channel names are stored in the file's metadata.

Next: how it works, the desktop app in detail, or every command-line option.