steinbock

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Document & test use with singularity

7

See #155

jwindhager

Segmentation fault in python package

6

Hi, I am trying to use steinbock in HPC, which is installed in a python 3.8 conda environment. The steinbock and the dependencies are installed through pip and the requirement.txt...

ynanli

Using the preprocess external option with large images

6

I have encountered this error below using the preprocess external option on large images? Note that I have used this option before with no issues. 1- I convert the original...

mjseignon

[Bug]No neighborhood Data in h5ad-files?

1

Hi, when exploring the .h5ad-file generated by `steinbock export anndata --intensities intensities --data regionprops --neighbors neighbors -o objects.h5ad` I've noticed that it doesn't contain any neighborhood-data. There exists a neighbors...

albert180

Maximum amount of segmented cells bounded from segmentation output file format (16-bit unsigned integer TIFF images)

3

Hi, I am running the following command: `steinbock segment deepcell --minmax` On a big image, it works fine and segments the image quite well. However, after the segmentation reaches the...

asom

Hi @Milad4849, a few things and thanks a lot in advance for clarification: 1. I realized that for the cellpose-"flavours" of steinbock the **"tissuenet" model** is not supported (despite being...

lassedochreden

It would be nice if steinbock could parse [cytomarker](https://cytomarker.ai) panels

jwindhager

Add option to remove the first acquisition row in IMC images.

1

Due to the laser, we often observe higher intensities in the first row (X = 1) of IMC images. I would suggest to add an argument for the `preprocess` functionality...

nathansteenbuck

Following the merge and release of https://github.com/BodenmillerGroup/readimc/pull/19, it would be great to add a `--strict/--no-strict` boolean option to the `steinbock preprocess imc images` command.

jwindhager

Hi, Last week, on a CYX image, I was able to get the code below to process the external image: `steinbock="singularity run -B /X/$FOLDER:/data --env STEINBOCK_MASK_DTYPE=uint32 docker://ghcr.io/bodenmillergroup/steinbock:0.16.1 ` where $FOLDER...

paulrbuckley-kcl