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https://github.com/keller-mark/nanosaber-mcmicro

Last synced: 12 days ago
JSON representation

Host: GitHub
URL: https://github.com/keller-mark/nanosaber-mcmicro
Owner: keller-mark
Created: 2021-04-09T15:09:42.000Z (almost 4 years ago)
Default Branch: main
Last Pushed: 2021-07-21T20:18:40.000Z (over 3 years ago)
Last Synced: 2024-11-13T06:22:12.428Z (2 months ago)
Language: Jupyter Notebook
Size: 54 MB
Stars: 0
Watchers: 1
Forks: 0
Open Issues: 0
Metadata Files:
- Readme: README.md

Awesome Lists containing this project

README

# nanosaber mcmicro example

## Installation on Mac

Install Java with JDK: https://adoptopenjdk.net/

```sh
# Install Nextflow
curl -s https://get.nextflow.io | bash
```

Move the Nextflow executable to a directory in your PATH.

Install bioformats: download the command-line tools from http://www.openmicroscopy.org/bio-formats/downloads/

Move the `bftools` directory to `~/software/bftools`

Install the Python environment:

```sh
conda env create -f environment.yml
conda activate nanosaber-mcmicro-env
```

Set the path to FIJI at the top of the Snakefile.

## Run the pipeline

```sh
snakemake -j 1
jupyter lab ./fc_all.ipynb
```

### Prepare for visualization with Vitessce

Open the registered 12-channel TIFF in ImageJ to convert the Z-stack to a channel stack.
- Image -> Hyperstacks -> Stack to Hyperstack
- 12 channel slices, 1 z slice, Composite display mode

Convert TIFF files to OME-TIFF using bioformats

```sh
bash ~/software/bftools/bfconvert ./data/lung_1_1/registration/lung_1_1.tif ./data/lung_1_1/registration/lung_1_1.ome.tiff

bash ~/software/bftools/bfconvert ./data/lung_1_1/segmentation/unmicst-lung_1_1/cellMask.tif ./data/lung_1_1/segmentation/unmicst-lung_1_1/cellMask.ome.tiff

tiffcomment ./data/lung_1_1/registration/lung_1_1.ome.tiff > ./data/lung_1_1/registration/lung_1_1.in.ome.xml
python add_channel_names.py -s lung_1_1
tiffcomment -set './data/lung_1_1/registration/lung_1_1.out.ome.xml' ./data/lung_1_1/registration/lung_1_1.ome.tiff
```

```sh
bash ~/software/bftools/bfconvert ./data/lung_2_1/registration/lung_2_1.ome.tif ./data/lung_2_1/registration/lung_2_1.ome.tiff

bash ~/software/bftools/bfconvert ./data/lung_2_1/segmentation/unmicst-lung_2_1/cellMask.tif ./data/lung_2_1/segmentation/unmicst-lung_2_1/cellMask.ome.tiff

tiffcomment ./data/lung_2_1/registration/lung_2_1.ome.tiff > ./data/lung_2_1/registration/lung_2_1.in.ome.xml
python add_channel_names.py -s lung_2_1
tiffcomment -set './data/lung_2_1/registration/lung_2_1.out.ome.xml' ./data/lung_2_1/registration/lung_2_1.ome.tiff
```

```sh
bash ~/software/bftools/bfconvert ./data/lung_2_2/registration/lung_2_2.tif ./data/lung_2_2/registration/lung_2_2.ome.tiff

bash ~/software/bftools/bfconvert ./data/lung_2_2/segmentation/unmicst-lung_2_2/cellMask.tif ./data/lung_2_2/segmentation/unmicst-lung_2_2/cellMask.ome.tiff

tiffcomment ./data/lung_2_2/registration/lung_2_2.ome.tiff > ./data/lung_2_2/registration/lung_2_2.in.ome.xml
python add_channel_names.py -s lung_2_2
tiffcomment -set './data/lung_2_2/registration/lung_2_2.out.ome.xml' ./data/lung_2_2/registration/lung_2_2.ome.tiff
```

## Vitessce instances

### Local

http://localhost:3000/?dataset=nanosaber-lung_1_1

http://localhost:3000/?dataset=nanosaber-lung_2_1

http://localhost:3000/?dataset=nanosaber-lung_2_2

### Cloud

Lung 1.1

```
https://s3.amazonaws.com/vitessce-data/demos/2021-05-24/a1802c9/index.html?url=data:,{"name":"lung_1_1","version":"1.0.1","description":"","public":true,"datasets":[{"uid":"lung_1_1","name":"lung_1_1","description":"lung_1_1","files":[{"type":"raster","fileType":"raster.json","options":{"schemaVersion":"0.0.2","usePhysicalSizeScaling":false,"images":[{"name":"Mask","type":"ome-tiff","url":"https://storage.googleapis.com/vitessce-demo-data/nanosaber-mcmicro/lung_1_1/segmentation/unmicst-lung_1_1/cellMask.ome.tiff","metadata":{"isBitmask":true,"transform":{"matrix":[1.0331,0,0,0,0,1.0331,0,0,0,0,1,0,0,0,0,1]}}},{"name":"Image","type":"ome-tiff","url":"https://storage.googleapis.com/vitessce-demo-data/nanosaber-mcmicro/lung_1_1/registration/lung_1_1.ome.tiff","metadata":{"isBitmask":false}}],"renderLayers":["Image","Mask"]}},{"type":"cell-sets","fileType":"cell-sets.json","url":"https://storage.googleapis.com/vitessce-demo-data/nanosaber-mcmicro/lung_1_1/flowcore/lung_1_1.cell-sets.json"},{"type":"cells","fileType":"cells.json","url":"https://storage.googleapis.com/vitessce-demo-data/nanosaber-mcmicro/lung_1_1/flowcore/lung_1_1.cells.json"}]}],"initStrategy":"auto","coordinationSpace":{},"layout":[{"component":"description","x":0,"y":0,"w":2,"h":1},{"component":"layerController","x":10,"y":0,"w":2,"h":4},{"component":"status","x":0,"y":1,"w":2,"h":1},{"component":"spatial","coordinationScopes":{},"x":2,"y":0,"w":8,"h":4},{"component":"cellSets","x":0,"y":2,"w":2,"h":2}]}
```

Lung 2.1

```
https://s3.amazonaws.com/vitessce-data/demos/2021-05-24/a1802c9/index.html?url=data:,{"name":"lung_2_1","version":"1.0.1","description":"","public":true,"datasets":[{"uid":"lung_2_1","name":"lung_2_1","description":"lung_2_1","files":[{"type":"raster","fileType":"raster.json","options":{"schemaVersion":"0.0.2","usePhysicalSizeScaling":false,"images":[{"name":"Mask","type":"ome-tiff","url":"https://storage.googleapis.com/vitessce-demo-data/nanosaber-mcmicro/lung_2_1/segmentation/unmicst-lung_2_1/cellMask.ome.tiff","metadata":{"isBitmask":true,"transform":{"matrix":[1.0234,0,0,0,0,1.0234,0,0,0,0,1,0,0,0,0,1]}}},{"name":"Image","type":"ome-tiff","url":"https://storage.googleapis.com/vitessce-demo-data/nanosaber-mcmicro/lung_2_1/registration/lung_2_1.ome.tiff","metadata":{"isBitmask":false}}],"renderLayers":["Image","Mask"]}},{"type":"cell-sets","fileType":"cell-sets.json","url":"https://storage.googleapis.com/vitessce-demo-data/nanosaber-mcmicro/lung_2_1/flowcore/lung_2_1.cell-sets.json"},{"type":"cells","fileType":"cells.json","url":"https://storage.googleapis.com/vitessce-demo-data/nanosaber-mcmicro/lung_2_1/flowcore/lung_2_1.cells.json"}]}],"initStrategy":"auto","coordinationSpace":{},"layout":[{"component":"description","x":0,"y":0,"w":2,"h":1},{"component":"layerController","x":10,"y":0,"w":2,"h":4},{"component":"status","x":0,"y":1,"w":2,"h":1},{"component":"spatial","coordinationScopes":{},"x":2,"y":0,"w":8,"h":4},{"component":"cellSets","x":0,"y":2,"w":2,"h":2}]}
```

Lung 2.2

```
https://s3.amazonaws.com/vitessce-data/demos/2021-05-24/a1802c9/index.html?url=data:,{"name":"lung_2_2","version":"1.0.1","description":"","public":true,"datasets":[{"uid":"lung_2_2","name":"lung_2_2","description":"lung_2_2","files":[{"type":"raster","fileType":"raster.json","options":{"schemaVersion":"0.0.2","usePhysicalSizeScaling":false,"images":[{"name":"Mask","type":"ome-tiff","url":"https://storage.googleapis.com/vitessce-demo-data/nanosaber-mcmicro/lung_2_2/segmentation/unmicst-lung_2_2/cellMask.ome.tiff","metadata":{"isBitmask":true,"transform":{"matrix":[1.167,0,0,0,0,1,0,0,0,0,1,0,0,0,0,1]}}},{"name":"Image","type":"ome-tiff","url":"https://storage.googleapis.com/vitessce-demo-data/nanosaber-mcmicro/lung_2_2/registration/lung_2_2.ome.tiff","metadata":{"isBitmask":false}}],"renderLayers":["Image","Mask"]}},{"type":"cell-sets","fileType":"cell-sets.json","url":"https://storage.googleapis.com/vitessce-demo-data/nanosaber-mcmicro/lung_2_2/flowcore/lung_2_2.cell-sets.json"},{"type":"cells","fileType":"cells.json","url":"https://storage.googleapis.com/vitessce-demo-data/nanosaber-mcmicro/lung_2_2/flowcore/lung_2_2.cells.json"}]}],"initStrategy":"auto","coordinationSpace":{},"layout":[{"component":"description","x":0,"y":0,"w":2,"h":1},{"component":"layerController","x":10,"y":0,"w":2,"h":4},{"component":"status","x":0,"y":1,"w":2,"h":1},{"component":"spatial","coordinationScopes":{},"x":2,"y":0,"w":8,"h":4},{"component":"cellSets","x":0,"y":2,"w":2,"h":2}]}
```