https://github.com/keller-mark/vitessce-mesmer-processing

https://github.com/keller-mark/vitessce-mesmer-processing

Last synced: 12 days ago
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• Host: GitHub
• URL: https://github.com/keller-mark/vitessce-mesmer-processing
• Owner: keller-mark
• Created: 2021-10-22T20:45:23.000Z (over 3 years ago)
• Default Branch: main
• Last Pushed: 2021-10-25T14:15:12.000Z (about 3 years ago)
• Last Synced: 2024-11-13T06:13:28.625Z (2 months ago)
• Language: Jupyter Notebook
• Size: 6.84 KB
• Stars: 1
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
Download data from https://deepcell.org/predict and put in new folder `data/raw`:

```

data

  -> raw

    -> vectra_breast_cancer.tif

       vectra_breast_cancer_feature_0.tif

       vectra_breast_cancer_feature_1.tif

```

Create and activate the Python environment using `conda`:

```sh

conda env create -f environment.yml

conda activate vitessce-mesmer-processing

```

Update paths to software: https://github.com/keller-mark/vitessce-mesmer-processing/blob/main/Snakefile#L12

- FIJI

- bioformats tools

Update path to data directory: https://github.com/keller-mark/vitessce-mesmer-processing/blob/main/src/t_to_c.js#L1

Process the images for visualization:

```sh

snakemake -j 1

```

Run the jupyter notebook for visualization:

```sh

jupyter lab

```