Desktop app

mcd_gui opens a window over the same engine as mcd_process: choose a file or a folder, pick regions, channels and outputs, and press Run.

mcd_gui

User guide, at the top right of the window, opens this page; so does the F1 key.

One file or a batch

The switch at the top of Input sets the mode.

• Single file — one .mcd file. Browse… opens a file picker, or paste a path into the box.
• Batch — a folder of .mcd files, or several files pasted as quoted paths (what Windows Explorer's Copy as path gives you). A file list opens on the left:
  • click the ✓ column to include or leave out a file;
  • click a file's name to show its regions and channels.

A batch during a run: sample_01 is done, sample_02 is running, and sample_04 is the file on show.

Save to is optional. Left empty, results go to MCD_Processed/ next to the input; the line underneath shows exactly where.

Regions and channels

Both tables are checklists. Every row starts ticked; click a row to leave it out, or use All and None.

• Regions you leave out are not converted or stitched.
• Channels you leave out give an extra _filtered copy of each output, holding only the ticked channels. The full files are still written. Here the background and calibration channels are left out.
• In a batch, region picks belong to each file. Channel picks do too, unless you tick Apply these picks to every file, which copies them to the other files by channel name. A warning appears when the ticked files do not all share one channel panel.
• Panoramas always cover the whole slide, whatever is ticked in the tables.

Outputs

Output	What you get
Convert	One OME-TIFF per region.
Stitch	All regions on one canvas.
Panoramas	The slide panoramas as PNG images, with region outlines drawn on large ones.
Pyramid	A copy of each converted or stitched file stored as tiles at several resolutions, for smooth panning and zooming. Needs Convert or Stitch.

With channels left out and Pyramid ticked, each output gets one _filtered_pyramid copy: the channel subset, stored as a pyramid.

Advanced settings

Click Advanced settings to show them.

Setting	Default	What it does
Data type	uint16	Pixel type of the OME-TIFFs: uint16 or float32.
Compression	zstd	zstd, LZW or None.
Memory cap	automatic	How much memory a run plans for, e.g. 8G. Left empty, the detected limit is used (shown in grey). See Memory.
Save a log file	off	Writes mcd_stitcher.log into the output folder.
Overwrite existing files	off	When off, a file whose outputs are already there is skipped.

Running and stopping

Press Run to start. The inputs grey out and lock until the run ends, and the bar and the line under it follow progress. In a batch, each file in the list turns cyan while it runs, then green when done, red if it failed, or amber if it was stopped part-way.

• Stop halts at the next safe point, after the region or copy being written. Files already finished are kept; a half-built stitched canvas is discarded.
• Force stop, a second click, ends the run at once and deletes any file it left half-written.

Running; after Stop, with Force stop on offer; and the message a force stop leaves.

Your system's notification sound plays when a run finishes, and Open output folder shows the results.

Updates

When the app opens, it checks whether a newer version is out. If one is, a window names it, links to what's new in it, and asks whether to update now:

• Yes closes the app, installs the new version and opens it again. If the update can't finish, a small window says why, and the version you had keeps working.
• No asks again the next time the app opens.
• Skip this version stays quiet until a later version comes out.

Without an internet connection, the app opens as usual.