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nf-artist

Nextflow Launch on Nextflow Tower run with docker GitHub Actions CI Status GitHub Actions Workflow Test Status Container Scan Status

A NextFlow pipeline to generate visualizations of multiplexed tissue imaging datasets. Initially developed for the HTAN Data Portal.

  • Converts bioformats files into OME-TIFF
  • Sets thresholds for each channel and pepares 4-channel overlay groups using Auto-Minerva
  • Renders a Minerva story using Minerva Author
  • Renders a thumbnail image using Miniature

A Docker container (ghcr.io/sage-bionetworks-workflows/nf-artist) is used to ensure reproducibility.

Example usage

nextflow run Sage-Bionetworks-Workflows/nf-artist --input <path-to-samplesheet> --outdir <output-directory>

Output

nf-artist outputs the following directory structure into the specified output directory (outdir):

├── outdir
│   ├── <simpleName or id for first row of samplesheet>
│   │   ├── thumbnail.jpeg
│   │   ├── minerva
│   │   │   ├── index.html
│   │   │   ├── exhibit.json
│   │   │   ├── story.json
│   │   │   ├── Group-1
│   │   │   │   ├── tile1.jpeg
│   │   │   │   ├── ...
│   │   │   ├── Group-<n>
│   │   │   │   ├── tile1.jpeg
│   │   │   │   ├── ...
│   ├── < simpleName or id for n'th row of samplesheet>

Options

Input/Output Options:

  • input: Path to a CSV sample sheet. This parameter is required. (Type: String)

  • outdir: Specifies the directory where the output data should be saved. Default is "outputs". (Type: String)

Miniature Options:

  • remove_bg: Setting this to true will remove the non-tissue background. Default is true. (Type: Boolean)

  • level: Specifies the pyramid level used in thumbnails. Default is -1 (smallest). (Type: Integer)

  • dimred: The dimensionality reduction method used. Default is "umap". Options include "umap", "tsne", and "pca". (Type: String)

  • colormap: Specifies the colormap used. Ensure the colormap is compatible with the number of n_components selected. Default is "UCIE". 3D colormap options: "UCIE", "LAB", "RGB". 2D colormap options: "BREMM", "SCHUMANN", "STEIGER", "TEULING2", "ZIEGLER", "CUBEDIAGONAL". (Type: String)

  • n_components: Specifies the number of components. Default is 3. Options are 2 and 3. (Type: Integer)

Samplesheet requirements

The samplesheet specified in the input parameter should be a CSV file with the following columns

  • image: [string] Path or URI to image to be processed
  • convert: [boolean] Should the image be converted to a OME-TIFF
  • he: [boolean] Is the image a H&E image
  • minerva: [boolean] Should a Minerva story be generated
  • miniature: [boolean] Should a Miniature thumbnail be generated
  • id: optional [string] A custom identifier to replace image simpleName in output directory structure