cluster_tools

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Hello, Will it be possible to have input data for the axon_dendrite_attribution experiment? I am following your code implementation here: https://github.com/constantinpape/cluster_tools/tree/master/publications/leveraging_domain_knowledge/1_axon_dendrite_attribution However, the link under “obtaining the data” for experiment...

daniJb

AssertionError: [30, 256, 256], (16, 128, 128

2

I am getting the following error when attempting to replicate results in the example folder: File "/ibex/scratch/bogesdj/miniconda/envs/cluster_env/lib/python3.10/site-packages/cluster_tools/write/write.py", line 88, in run_impl assert all(bs % ch == 0 for bs, ch...

daniJb

threadpool issue

11

Hi, I am trying to set up mboie_utils on Windows and Python 3.9 (fresh mamba installation, no other packages). I run into: ``` ...\cluster_tools\watershed\watershed.py", line 140, in @threadpool_limits.wrap(limits=1) # restrict...

martinschorb

Hi @constantinpape , I tried to implement what you suggested here https://github.com/constantinpape/cluster_tools/pull/42#issuecomment-1807688915 in mobie-utils-python` but found that `fit_to_roi` seems to be ignored by `copy_volume`. The resulting file still has full...

martinschorb

We need to ensure that the axis metadata can be passed correctly to ome.zarr files. This can be passed via `metadata_dict` https://github.com/constantinpape/cluster_tools/blob/master/cluster_tools/downscaling/downscaling_workflow.py#L19. But I am not sure if this is...

constantinpape

No such file or directory

1

Hi, @constantinpape , thank you for this great project! I tried to compute multicut segmentation using the provided example data and `multicut.py` on a SLURM cluster. However, after many attempts,...

XiaoyiAce