Eric Jelli

Fix bug with single object masks

3

During one of my GPU model trainings I ran into a problem in `cellpose/dynamics.py`. The line: https://github.com/MouseLand/cellpose/blob/e6d7d2e73fe27754288de1fb30ea71bf295930e9/cellpose/dynamics.py#L88 fails if a label image contains only a single object since `squeeze` operates...

WIP: Enable (local) GPU testing

2

Hi, during my last development sessions on the code, I realized that the GPU implementation is a blind spot in the test routines. While github-hosted runners do not come with...

Adaptation to EM samples with extracellular space

1

Hi, I wonder whether there are ideas around to deal with 'non-dense' EM datasets. In the ISBI dataset (left) the objects are directly touching each other. In my dataset (right)...

Hi, I tried to upload annotations with a `fallback_layer` included: ```python # test.py import webknossos as wk fallback_layer = wk.Dataset\ .open_remote('https://webknossos.org/datasets/Demo_Organization/kasthuri2011')\ .get_segmentation_layers()[0] annotation = wk.Annotation( name="test_annotation", dataset_name = fallback_layer.dataset.name, voxel_size...

### Description: If an annotation is merged with a compressed fallback layer, the bounding box of the `output_mag` needs to account for compressed shard writes outside the original bounding box...

Expose squeue polling interval to SlurmExecutor parameter and allow setting via env variable

1

Hi, we regularly run into problems with our SLURM cluster while running (very) large downsampling jobs on webknossos datasets either via CLI or chunk-wise processing of large datasets via the...

I cannot read datasets created with version 0.14.25 onward with version 0.14.24. Error message: ``` >>> import webknossos as wk >>> wk.Dataset.open('my_newer_dataset') + Exception Group Traceback (most recent call last):...

Tested code for for python > 3.9 and numpy >= 2.0

4

Hi, I don't know whether I will regret this in the future, but I decided to port the repository to recent python (currently 3.12), numpy (2.0.2), and opencv-python (4.10). All...

Gracefully exit rank != 0 job steps on slurm cluster

2

Hi, first, thanks for open sourcing `submitit`! It simplifies the setup of distributed cluster jobs on our inhouse slurm cluster a lot. ### Some context: While requeuing 32 node jobs,...

Hi 👋 , thank you for providing `imagecorruptions` as open source package via github and via pypi! I try to bring the (currently unmaintained) package [imgaug](https://github.com/aleju/imgaug) back to live. Fortunately...