steinbock

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Completely black masks from deepcell

1

Hi, I have been working through your pipeline and have passed my .tiff images extracted from raw .mcd files to deepcell for object segmentation via steinbock. In my panel file,...

paulrbuckley-kcl

See #155

jwindhager

Deepcell command not found

6

deepcell command is not found for the most updated steinbock package (0.15.0)

sshin48

Include napari in Docker container

4

jwindhager

Segmentation issues

6

There are few issues running steinbock: Once I have # Select a random image rng = np.random.default_rng() ix = rng.choice(len(segstacks)) I see a value error (ValueError: a must be a...

KHALILISAEED

Examples

6

jwindhager

intensities/regionprops measurement of potentially corrupted TIFF files crashes with empty error message

1

@MureziCapaul

jwindhager

``` ERROR steinbock.preprocessing.imc - Error reading file raw/20220819_MC_NSCLCTcellexh_87C_1/20220819_MC_NSCLCTcellexh_87C_1/20220819_MC_NSCLC_Tcellexh_87C_1.mcd: sequence item 0: expected str instance, PosixPath found Traceback (most recent call last): File "/app/steinbock/steinbock/preprocessing/imc.py", line 341, in _try_preprocess_mcd_images_from_disk recovery_txt_file = _match_txt_file(...

jwindhager

mask expansion

3

nuclear segmentation followed by a simple user defined mask expansion would be a nice feature for future releases.

SchulzDan

Comparison of neighbour detection to CellProfiler

5

Hey, I came around to test the similarity between the CellProfiler neighbour detection approach (mask expansion) to `steinbock measure neighbors --type expansion --dmax `. This is just for documentation purposes...

nilseling