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Hi,
I was able to run the entire Stereocell pipeline, but when taking a look at the nuclei segmentation and the transcripts assigned to each cell, I noticed that many times, a few nuclei are being …
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When I run through your pipeline, there is always an error of
Traceback (most recent call last):
File "/import/home2/yhchenmath/Code_raw/BIDCell-main/run.py", line 3, in
model.run_pipeline(…
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# StarDist Fluorescence Nuclei Segmentation
Bioimage.io -- an AI model repository for deep learning.
[https://bioimage.io/?partner=ilastik&type=model&id=10.5281%2Fzenodo.6348084](https://bioimage.io…
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Hi,
I'm trying to run the Nuclei Segmentation step on a Visium image with shape (9847, 10090), but I receive the following error message:
```python
terminate called after throwing an instance…
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### Nuclei version:
latest (3.2.9)
### Current Behavior:
SIGSEGV when running workflow that includes template using headless protocol despite not enabling headless
### Expect…
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Hi Devs, thanks for this repo!
Are contributions to the nuclei segmentation part using an external library allowed? For example using CellPose or something similar.
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People who work in cell analysis have reported to me in a private conversation that they achieve very high using EfficientNet by Google as the network architecture. Additionally, the network uses very…
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Hi pipeline creator,
I am new to IMC data analysis so please bear my ignorance. My query related to this- https://bodenmillergroup.github.io/ImcSegmentationPipeline/ilastik.html
While trying to im…
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Set the epoch to 20, but why did it stop once
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Hi!
Thanks for sharing. I am trying to train the model on a dataset with only one nuclei type. If I set the num_nuclei_classes =2, does the branch for nuclei type prediction get constructed? I will…