JaneliaSciComp/bigstitcher
modulePerforms 3-D multi-tile and multi-angle alignment using BigStitcher-Spark
spark stitching BigStitcher
BioImageTools Nextflow Module Catalog
Find reusable Nextflow modules and subworkflows for bioimaging workflows.
All Modules
57 modules available
JaneliaSciComp/bigstream_registration
subworkflowRuns a registration pipeline using Bigstream on a Dask cluster
registration bigstream dask
Convert any Bioformats-compatible image to OME-Zarr format
image formats converter OME-Zarr
BioImageTools/cellpose
modulePerforms a 3-D segmentation using cellpose distributed on a dask cluster
dask segmentation cellpose
JaneliaSciComp/cellpose
modulePerforms a 3-D segmentation using cellpose distributed on a dask cluster
dask segmentation cellpose
JaneliaSciComp/dask_start
subworkflowCreates a Dask cluster and waits for it to be ready
dask infrastructure distributed
BioImageTools/dask_startcluster
subworkflowCreates a Dask cluster and waits for it to be ready
dask infrastructure
BioImageTools/dask_startcluster
subworkflowCreates a Dask cluster and waits for it to be ready
dask infrastructure
BioImageTools/dask_startcluster
subworkflowCreates a Dask cluster and waits for it to be ready
dask infrastructure
Start a Dask scheduler which runs until the terminate module is called
dask
BioImageTools/dask_terminate
moduleTerminate a Dask cluster by writing a marker file to the work dir
dask
Retrieve dask cluster info from the JSON file created by the scheduler
dask
Alignment by Simultaneous Harmonization of Layer/Adjacency Registration
image_processing alignment registration
Concatenate multiple WKT files into one in a brutal way
wkt segmentation post-processing
cellgeni/imaging_deepcell
moduleThis module runs deepcell on a crop of an image
image analysis image segmentation imaging
Extract max intensity peak profile from an image stack with a file of peak coordinates
image
write your description here
sort example genomics
a helper script to generate tiles from an 2D image file
image tiling slicing
cellgeni/imaging_instanseg
moduleA wrapper of InstanSeg segmentation tool
image analysis segmentation instanseg
A simple python script to merge outlines from multiple overlapping tiles
image analysis merge polygons outlines shapely
cellgeni/imaging_mergepeaks
moduleMerge peaks from multiple peak files (csv)
peaks tiled_analysis imaging
Preprocess both profile to be decoded and the corresponding codebook for PoSTCode decoding
spatial transcriptomics decoding codebook starfish
cellgeni/microaligner_registration
subworkflowRegister microscopy images using two-step microaligner
linear registration non-linear registration microaligner
cellgeni/ml_xeniumharmonise
moduleA wrapper module for harmonise_xenium.py script
spatial-transcriptomics(xenium) ml he-image
cellgeni/nichecompass
subworkflowNicheCompass training & analysis
spatial_atlas_building niche_identification niche_characterisation cell-cell_communication_inference
+2 more
cellgeni/postcode_decoding
subworkflowSort SAM/BAM/CRAM file
spatial transcriptomics decoding postcode probabilistic decoding
JaneliaSciComp/rs_fish
modulePrecise, interactive, fast, and scalable FISH spot detection
spatial transcriptomics spatial genomics FISH
BioImageTools/spark_cluster
subworkflowCreates a Spark cluster and waits for it to be ready
spark bigdata infrastructure
BioImageTools/spark_start
subworkflowStarts Spark processing either by spinning up a cluster or setting up variables so that processing can run locally as individual jobs
spark bigdata infrastructure
JaneliaSciComp/spark_start
subworkflowStarts Spark processing either by spinning up a cluster or setting up variables so that processing can run locally as individual jobs
spark bigdata infrastructure
Start a Spark manager which runs until the terminate module is called
spark
Start a Spark worker which runs until the terminate module is called
spark
BioImageTools/spark_stop
subworkflowStops Spark processing by writing a marker file which terminates the cluster processes.
spark bigdata infrastructure
JaneliaSciComp/spark_stop
subworkflowStops Spark processing by writing a marker file which terminates the cluster processes.
spark bigdata infrastructure
Terminate a Spark cluster by writing a marker file to the work dir
spark
Analysis based on the NicheCompass model
spatial_atlas_building niche_identification niche_characterisation cell-cell_communication_inference
+3 more
Train a NicheCompass model on spatial multiomics data.
spatial_atlas_building niche_identification niche_characterisation cell-cell_communication_inference
+3 more
cellgeni/tiled_cellpose
subworkflowA tiled version of CellPose to faciliate processing of large images on HPC
cellpose segmentation instance segmentation deep-learning
+1 more
BioImageTools/yolo_detect
modulewrite your description here
machine-learning yolo image-detection bounding box
+1 more
JaneliaSciComp/bigstitcher module Performs 3-D multi-tile and multi-angle alignment using BigStitcher-Spark
JaneliaSciComp/bigstream_registration subworkflow Runs a registration pipeline using Bigstream on a Dask cluster
BioImageTools/cellpose module Performs a 3-D segmentation using cellpose distributed on a dask cluster
JaneliaSciComp/cellpose module Performs a 3-D segmentation using cellpose distributed on a dask cluster
BioImageTools/dask_startmanager module Start a Dask scheduler which runs until the terminate module is called
BioImageTools/dask_terminate module Terminate a Dask cluster by writing a marker file to the work dir
BioImageTools/dask_waitformanager module Retrieve dask cluster info from the JSON file created by the scheduler
cellgeni/imaging_ashlarcompanion module Alignment by Simultaneous Harmonization of Layer/Adjacency Registration
cellgeni/imaging_extractpeakprofile module Extract max intensity peak profile from an image stack with a file of peak coordinates
cellgeni/imaging_mergeoutlines module A simple python script to merge outlines from multiple overlapping tiles
cellgeni/imaging_postcodeprep module Preprocess both profile to be decoded and the corresponding codebook for PoSTCode decoding
cellgeni/microaligner_registration subworkflow Register microscopy images using two-step microaligner
BioImageTools/spark_start subworkflow Starts Spark processing either by spinning up a cluster or setting up
variables so that processing can run locally as individual jobs
JaneliaSciComp/spark_start subworkflow Starts Spark processing either by spinning up a cluster or setting up
variables so that processing can run locally as individual jobs
BioImageTools/spark_startmanager module Start a Spark manager which runs until the terminate module is called
BioImageTools/spark_startworker module Start a Spark worker which runs until the terminate module is called
BioImageTools/spark_stop subworkflow Stops Spark processing by writing a marker file which terminates the
cluster processes.
JaneliaSciComp/spark_stop subworkflow Stops Spark processing by writing a marker file which terminates the
cluster processes.
BioImageTools/spark_terminate module Terminate a Spark cluster by writing a marker file to the work dir
cellgeni/tiled_cellpose subworkflow A tiled version of CellPose to faciliate processing of large images on HPC
No modules match your filters. Try adjusting your search criteria.