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Here is an overview of current MoBIE projects, which have ome.zarr data and samples:
## Spatial Transcriptomics Data
https://github.com/mobie/mouse-embryo-spatial-transcriptomics-project
This…
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As pointed out in #177 , cellpose in ACDC doesn't support the second channel.
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Using the current implementation of separate clumps (version 0.1.1), a sizeable number of nuclei are lost. These nuclei then typically are within the cytoplasm of other cells.
The way this seems to…
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Dear author,
I read your paper 'Segmentation of Nuclei in Histopathology Images by deep regression of the distance map' and I found your dataset here. However, we proposed a method of post-process…
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Take a look at following issues:
- [x] Straightening process relative to existing data set
- [ ] Scaling new data set relative to existing data set -- with goal of having 3D representation of both d…
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Tasks to work on:
- Displaying both video together. Displaying two channels with two different colors?
- Working on automating threshold
- Work on tracking spots through time
- to reduce noise t…
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Hi,
I'm trying to use bTrack on cellpose cytoplasmic segmentation(no nuclei data) and visualize using napari. When I visually check the division events are detected fine (the parent number is ass…
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This code is not working,
```
name: Nuclei-Target-Workflow-Engine
on: [push]
jobs:
build:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- name: Run Nuclei
…
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Dear Kwok,
After running SEPIA for the participants, now I want to corregister the subject Chimap to AHEAD template. So, I used the SEPIA GUI for this but the problem is, it is very slow. I have used…
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## Use Case
Requested by Jessica and Graham!
They described an issue where, when doing a max-projection through a volume, cell nuclei (or cells) may be overlapping in the projection. Currently, th…