Jonas Windhager

Hey @jul1an-o, apologies for the late reply! Unfortunately, the current steinbock `Dockerfile` installs the official build of TensorFlow that requires CPU hardware supporting Advanced Vector Extensions (AVX), which is not...

Hi @ynanli, I assume you are installing steinbock as a Python package, instead of using the steinbock Docker container. If you do so, you need to make sure that deepcell...

I don't think that this would explain the segfault, but you will indeed need to download the model locally in case you don't have an internet connection. You can have...

Since you're using Singularity, you'll need to specify the `STEINBOCK_MASK_DTYPE` environment variable with `--env`: ```bash singularity run --env STEINBOCK_MASK_DTYPE=uint32 -B /sc:/sc docker://ghcr.io/bodenmillergroup/steinbock:0.16.1 segment deepcell --img img --minmax --panel panel.csv -o...

Note: IIRC this happens because, for the first row, the laser does not just ablate the "stage delta", but the full spot size.

Hi @paulrbuckley-kcl! Your commands look right to me. I suspect that the TIFF shape is not compatible with steinbock (expected dimension order: CYX, optionally with additional dimensions of size 1...

Hi both, sorry for not getting back to you earlier. As commented, I've only reviewed the documentation-related issues so far. Will now take a closer look at the code changes...

Hi @Milad4849! Apologies for the delay, I completely missed that you re-requested a review. Will do it asap, latest at the end of this week. CC @SchulzDan

Also, the code still contains `#TODO` for list-like options

Something like this should work starting from steinbock 0.16.0 (untested): singularity run --bind /mnt/data/git/steinbock/data:/data --env RUN_FIXUID= docker://ghcr.io/bodenmillergroup/steinbock:0.16.0 This may also make running GUI applications such as napari much easier.