Find reusable Nextflow modules and subworkflows for bioimaging workflows.
BaSiCPy is a python package for background and shading correction of optical microscopy images. It is developed based on the Matlab version of BaSiC tool with major improvements in the algorithm.
Extract OME xml data from OME-tif
Performs 3-D multi-tile and multi-angle alignment using BigStitcher-Spark
Compute the inverse of a local deformation field using Bigstream
Apply local deformation (and optional affine) transforms to warp a moving image onto a fixed image using Bigstream
Apply local deformation (and optional affine) transforms to warp a moving image onto a fixed image using Bigstream
Generate a foreground mask for a 3-D volume using Bigstream
Global affine alignment of a 3-D volume using Bigstream
Local deformable alignment of a 3-D volume using Bigstream
Runs a registration pipeline using Bigstream on a Dask cluster
Apply affine and deformation transforms to coordinate sets using Bigstream
Convert any Bioformats-compatible image to OME-Zarr format
Java application to convert image file formats, including .mrxs, to an intermediate Zarr structure compatible with the OME-NGFF specification.
Performs a 3-D segmentation using cellpose distributed on a dask cluster
cellpose segments cells in images using GPU-accelerated deep learning
Creates a Dask cluster and waits for it to be ready
Creates a Dask cluster and waits for it to be ready
Creates a Dask cluster and waits for it to be ready
Creates a Dask cluster and waits for it to be ready
Start a Dask scheduler which runs until the terminate module is called
Terminate a Dask cluster by writing a marker file to the work dir
Retrieve dask cluster info from the JSON file created by the scheduler
Deepcell/mesmer segmentation for whole-cell
Alignment by Simultaneous Harmonization of Layer/Adjacency Registration
Concatenate multiple WKT files into one in a brutal way
This module runs deepcell on a crop of an image
Extract max intensity peak profile from an image stack with a file of peak coordinates
a helper script to generate tiles from an 2D image file
A wrapper of InstanSeg segmentation tool
A simple python script to merge outlines from multiple overlapping tiles
Merge peaks from multiple peak files (csv)
Preprocess both profile to be decoded and the corresponding codebook for PoSTCode decoding
Staging module transforming Imaging Mass Cytometry .txt files to .tif files with OME-XML metadata. Includes optional hot pixel removal.
Staging module for MCMICRO transforming Imaging Mass Cytometry .txt files to .tif files with OME-XML metadata. Includes optional hot pixel removal.
Staging module for MCMICRO transforming MACSima data sets for being registered with ASHLAR in MCMICRO.
Staging module for MCMICRO transforming PhenoImager .tif files into stacked and normalized ome-tif files per cycle, compatible as ASHLAR input.
Export METASPACE datasets to AnnData and SpatialData objects
Register microscopy images using two-step microaligner
marks duplicate spots along gridline edges.
Takes a single panorama image and fills the empty grid lines with neighbour-weighted values.
A wrapper module for harmonise_xenium.py script
Contrast-limited adjusted histogram equalization (CLAHE) on single-channel tif images.
NicheCompass training & analysis
Generates a multiscale pyramid for an OME-Zarr container
Formatting PhenoImager TIFF output files into stacked and normalized OME-TIFF files per cycle, compatible as ASHLAR and MCMICRO input.
Sort SAM/BAM/CRAM file
A module to generate images from Pretext contact maps.
Performs a 3-D segmentation using cellpose distributed on a dask cluster
Merge labels across block boundaries after a 3-D distributed segmentation
Module to use the 10x Space Ranger pipeline to process 10x spatial transcriptomics data
Creates a Spark cluster and waits for it to be ready
Starts Spark processing either by spinning up a cluster or setting up variables so that processing can run locally as individual jobs
Starts Spark processing either by spinning up a cluster or setting up variables so that processing can run locally as individual jobs
Start a Spark manager which runs until the terminate module is called
Start a Spark worker which runs until the terminate module is called
Stops Spark processing by writing a marker file which terminates the cluster processes.
Stops Spark processing by writing a marker file which terminates the cluster processes.
Terminate a Spark cluster by writing a marker file to the work dir
Analysis based on the NicheCompass model
Train a NicheCompass model on spatial multiomics data.
Spotiflow, accurate and efficient spot detection with stereographic flow.
Detects FISH spots in an OME-Zarr image using the easifish spot extraction pipeline
Precise, interactive, fast, and scalable FISH spot detection
Cell and nuclear segmentation with star-convex shapes
Perform segmentation of MERSCOPE TIFF images using the vizgen-postprocessing tool
A tiled version of CellPose to faciliate processing of large images on HPC
The module compiles segmentation tiles using Vizgen's post-processing tool.
The module prepares the specification JSON file for Vizgen's post-processing tool cell segmentation workflow.
The module runs the segmentation algorithm on a specific tile using Vizgen's post-processing tool.
The xeniumranger import-segmentation module runs `xeniumranger import-segmentation` to recompute Xenium Onboard Analysis outputs using external segmentation results. It supports two execution modes mirroring the Xenium Ranger CLI: an image-based mode that accepts nuclei and/or cell masks (TIFF/NPY) or GeoJSON polygons together with optional coordinate transforms and unit definitions, and a transcript-based mode that ingests Baysor-style transcript assignment CSV files plus visualization polygons. Use the image-based inputs when providing label masks or polygons, or switch to the transcript-based inputs when supplying transcript-level assignments so the appropriate command-line arguments are passed to Xenium Ranger.
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