Write segementation masks with Mesmer in 32bit to segement larger ablation areas.

[mabar1]

Dear Steinbock community,
we ablated bigger-than normal IMC tissues with up to 2000x4000px and run into the problem that the 16bit segmentation masks produced via
steinbock segment deepcell --minmax
do not have enough bit-depth. I saw the issues 207 and 132 and I am wondering how to adapt the above command to produce 32bit tiffs.
We are using docker and command line, so I assume one needs to supply STEINBOCK_MASK_DTYPE to
doskey steinbock=docker run -p 8888:8888 -v "pathtodata":/data ghcr.io/bodenmillergroup/steinbock:0.16.1 $*
Did anyone succeed in creating 32bit segementation maps from Steinbock running in docker?
Best, matthias

[Milad4849]

Hi @mabar1

First off, apologies, the relevant documentation is missing and will be added with the new release. Please modify your docker alias command: doskey steinbock = docker run -e STEINBOCK_MASK_DTYPE=uint32 ....

[mabar1]

Dear Milad4849,
that is exactly what I needed, thank you very much. I will test it later on.
Thank you for the fast answer!