Running mcquant Without mcmicro – Issues with Segmented TIFFs and Channel Markers

[MartinOcharo]

Hello, and thank you for creating and maintaining this fantastic tool!

I'm trying to run mcquant independently of the full mcmicro pipeline using my own pre-segmented .tif files and channel marker CSV. However, I keep encountering errors during execution.

Here’s what I’m using:

• A segmented .tif file as the mask
• A raw image file (.ome.tif)
• A CSV file containing channel marker names

Could you please clarify:

• Whether mcquant can be run standalone (outside of mcmicro)
• What the expected input formats and structure are
• Any dependencies or setup steps I might be missing

Thank you in advance for your help!

[ArtemSokolov]

Hi @MartinOcharo,

What errors are you running into?
Are you running the tool through a Docker container or with a local installation?

If you have Docker installed, you can put all your input files into a single directory and run this command from that directory:

docker run --rm -v "$PWD":"$PWD" labsyspharm/quantification:1.6.0 \
  mcquant --image raw.ome.tif --masks cell.tif --channel_names channels.csv --output .

replacing raw.ome.tif, cell.tif and channels.csv with your filenames.

In the above,

• --rm will clean up the container after it's done executing
• -v "$PWD":"$PWD" will map the current directory containing your input files to be visible inside the container. Since the tool also writes to ., you should see the output files in that same directory after execution.