segger_dev

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updates: - https://github.com/psf/black → https://github.com/psf/black-pre-commit-mirror - [github.com/psf/black-pre-commit-mirror: 24.10.0 → 25.11.0](https://github.com/psf/black-pre-commit-mirror/compare/24.10.0...25.11.0) - [github.com/asottile/blacken-docs: 1.19.1 → 1.20.0](https://github.com/asottile/blacken-docs/compare/1.19.1...1.20.0)

pre-commit-ci[bot]

High memory and runtime requirements when adding scRNA-seq data

3

Hello, I’m trying to run Segger with the tutorial data. The pipeline runs fine (with reasonable memory and runtime) when I exclude the scRNA-seq data, but when I include it,...

asmariyaz23

Error during segment -- cudaErrorIllegalAddress

2

Hi, I get an error during segment step ``` segment( trained_model, dm_predict, save_dir=segmentation_output_dir, seg_tag='segger_output', transcript_file=xenium_data_dir / 'transcripts.parquet', receptive_field=receptive_field, min_transcripts=5, cell_id_col='segger_cell_id', use_cc=False, knn_method='kd_tree', verbose=True, save_cell_masks=False ) ``` The error is: `Processing...

pzumbo

EliHei2

Error when running seg2explorer

4

I installed the latest version of segger and ran into some issues with seg2explorer. ```pytb get_flatten_version(polygon_vertices, max_value) 29 flattened.append(vertices[:max_value]) 30 else: ---> 31 flattened.append(vertices + [(0.0, 0.0)] * (max_value -...

HarryZhang1224

[Error] Running seg2explorer

5

Dear segger team, Hi, all! Hope you been well and thanks for the sharing tool for community: I am running the most recent segger_dev repo. with Xenium_v2 dataset and have...

jpark27

Missed requirements

1

I have followed the installation requirements of segger but the following line reveals a few dependencies missed: `from segger.prediction.predict_parquet import segment, load_model ` and I could get this issue sorted...

mossishahi

[Visualisation] Baysor-like output

4

Hi, @EliHei2 ! Hope you been well. I've been testing `segger-dev` on in-house Xenium dataset as purpose of head-to-head comparison with Baysor. I have final output like following but somehow...

jpark27

CUDA error when running predictions without GPU

6

I am running segger in the `danielunyi42/segger_dev:cuda121` docker container on a system without gpu. The training went well by setting ```python trainer = Trainer( accelerator="cpu" ... ) ``` I then...

LouisK92

Spatialdata and dask Comatibility

1

hi segger dev team, i guess you can also confirm that the community which uses Segger is also a user of Spatialdata. I've been facing a requirement incompatibility between segger...

mossishahi