steinbock
steinbock copied to clipboard
BodenmillerGroup
Dockerized multi-channel image processing framework
Hi, I am running 'steinbock preprocess external images' on a CODEX-generated .ome.tiff, which has been exported from QuPath. When converting to 'steinbock file format' I receive the following warning and...
See [#197 ](https://github.com/BodenmillerGroup/steinbock/issues/197#issuecomment-1599163066)
The following lines should be changed to include the original exception potentially raised [here](https://github.com/BodenmillerGroup/steinbock/blob/bc10207a5a690254bb4e65089c06004fe3f19b05/steinbock/preprocessing/external.py#L20-L38): https://github.com/BodenmillerGroup/steinbock/blob/bc10207a5a690254bb4e65089c06004fe3f19b05/steinbock/preprocessing/external.py#L83-L84 For example similar to the following lines: https://github.com/BodenmillerGroup/steinbock/blob/bc10207a5a690254bb4e65089c06004fe3f19b05/steinbock/measurement/intensities.py#L65-L66
I re-ran the bash script shown here: ``` #!/usr/bin/env bash BASEDIR=$(cd -- "$(dirname "${BASH_SOURCE[0]}")" && pwd -P) cd "${BASEDIR}" # raw data collection mkdir raw wget https://zenodo.org/record/7997296/files/IMCWorkflow.ilp wget https://zenodo.org/record/7997296/files/analysis.zip unzip...
As reported by @cavenel, when running `steinbock export anndata` in concatenation mode (default) and with `--neighbors`, the resulting multi-image anndata object does not contain the spatial cell graphs in `obsp`....
The CellProfiler pipeline used in steinbock does not match the current pipeline in the ImcSegmentationPipeline.
Hi @jwindhager I tested the DeepCell implementation in steinbock on my Mac (OS Big Sur 11.6.2, Apple M1 chip). As reported [here](https://github.com/tensorflow/serving/issues/1948), tensorflow within docker is not supported on this...
Currently, the default behavior is `--no-mmap` (`default=False`) for commands that support memory mapping. Maybe we should consider changing this to `--mmap` (`default=True`), or to make the default behavior configurable using...
To export steinbock-supported TIFF files to OME-Zarr format. Examples for how OME-Zarr files can be written in Python can be found e.g. [here](https://github.com/BodenmillerGroup/mcd2zarr) (note that the direct use of mcd2zarr...
To extract panels from OME-TIFF or OME-Zarr metadata and convert images from the respective format to steinbock-supported TIFF files
Metadata
Owner
Metadata
Dockerized multi-channel image processing framework