nf-artist

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