Workflows

The present workflow allows to perform 2D spots/blobs detection on specific channel and stack of an image. Images will be directly fetched from IDR by including the IDs. A pre-processing steps with histogram normalization is performed before the blobs detection.

Associated Tutorial

This workflows is part of the tutorial Quantification of single-molecule RNA fluorescence in situ hybridization (smFISH) in yeast cell lines, ...

AnnData to Seurat format conversion (manually using Galaxy buttons)

Associated Tutorial

This workflows is part of the tutorial Converting between common single cell data formats, available in the GTN

Features

• Includes Galaxy Workflow Tests

Thanks

...

Associated Tutorial

This workflows is part of the tutorial Using BioImage.IO models for image analysis in Galaxy, available in the GTN

Features

• Includes Galaxy Workflow Tests
• Includes a [Galaxy Workflow ...

Trajectory analysis using Monocle3, starting from AnnData

Associated Tutorial

This workflows is part of the tutorial Inferring single cell trajectories with Monocle3, available in the GTN

Features

• Includes Galaxy Workflow Tests

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AnnData to SCE format conversion (manually using Galaxy buttons)

Associated Tutorial

This workflows is part of the tutorial Converting between common single cell data formats, available in the GTN

Features

• Includes Galaxy Workflow Tests

Thanks

...

Generic workflow to perform Voronoi segmentation. Input requirements:

• Image: -- Preferably lighter objects on a darker background for the mask to work well. -- Format: .tiff, stored in planar RGB format, not interleaved (http://avitevet.com/uncategorized/when-to-use-it-interleaved-vs-planar-image-data-storage/).
• Seeds: -- White seeds on a black background -- Format: .tiff

Associated Tutorial

This workflows is part of the tutorial [Voronoi ...

Preparing and filtering gene and cell annotations files and expression matrix to be passed as input for Monocle

Associated Tutorial

This workflows is part of the tutorial Inferring single cell trajectories with Monocle3, available in the GTN

Thanks to...

Tutorial Author(s): [Julia ...

Workflow based on clustering 3K PBMCs with Scanpy tutorial

Associated Tutorial

This workflows is part of the tutorial Clustering 3K PBMCs with Scanpy, available in the GTN

Features

• Includes Galaxy Workflow Tests
• Includes a [Galaxy Workflow ...

Workflows for comparison of genes in annotated genomes

Associated Tutorial

This workflows is part of the tutorial Comparative gene analysis in unannotated genomes, available in the GTN

Thanks to...

Workflow Author(s): Anton Nekrutenko

Tutorial Author(s): Anton Nekrutenko ...

Workflow to assess nuclei segmentation by applying different Gaussian filtering values during image pre-processing.

Associated Tutorial

This workflows is part of the tutorial Parameter tuning and optimization - Evaluating nuclei segmentation with Galaxy, available in the GTN

Features

• Includes [Galaxy Workflow ...