Nextflow Modules
Showing module(s) with keyword "imaging"
| Module | Keywords | Description |
|---|---|---|
| nf-core/basicpy | illumiation_correction background_correction microscopy imaging | 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. |
| nf-core/bftools/showinf | metadata ome-tif ome-tiff imaging bioinformatics tools | Extract OME xml data from OME-tif |
| nf-core/bioformats2raw | zarr ome-ngff imaging | Java application to convert image file formats, including .mrxs, to an intermediate Zarr structure compatible with the OME-NGFF specification. |
| nf-core/deepcell/mesmer | imaging spatial_omics segmentation | Deepcell/mesmer segmentation for whole-cell |
| nf-core/imc2mc | imaging ome-tif staging MCMICRO | Staging module transforming Imaging Mass Cytometry .txt files to .tif files with OME-XML metadata. Includes optional hot pixel removal. |
| nf-core/mcstaging/imc2mc | imaging ome-tif staging MCMICRO | Staging module for MCMICRO transforming Imaging Mass Cytometry .txt files to .tif files with OME-XML metadata. Includes optional hot pixel removal. |
| nf-core/mcstaging/macsima2mc | imaging ome-tif mcmicro staging spatial-omics macsima | Staging module for MCMICRO transforming MACSima data sets for being registered with ASHLAR in MCMICRO. |
| nf-core/mcstaging/phenoimager2mc | imaging registration ome-tif Staging MCMICRO | Staging module for MCMICRO transforming PhenoImager .tif files into stacked and normalized ome-tif files per cycle, compatible as ASHLAR input. |
| nf-core/metaspace/converter | anndata spatialdata metabolomics mass spectrometry imaging | Export METASPACE datasets to AnnData and SpatialData objects |
| nf-core/mindagap/duplicatefinder | imaging resolve_bioscience spatial_transcriptomics | marks duplicate spots along gridline edges. |
| nf-core/mindagap/mindagap | imaging resolve_bioscience spatial_transcriptomics | Takes a single panorama image and fills the empty grid lines with neighbour-weighted values. |
| nf-core/molkartgarage/clahe | clahe image_processing imaging correction | Contrast-limited adjusted histogram equalization (CLAHE) on single-channel tif images. |
| nf-core/phenoimager2mc | imaging registration ome-tif Staging MCMICRO | Formatting PhenoImager TIFF output files into stacked and normalized OME-TIFF files per cycle, compatible as ASHLAR and MCMICRO input. |
| nf-core/raw2ometiff | ome tiff imaging | write your description here |
| nf-core/spaceranger/count | align count spatial spaceranger imaging | Module to use the 10x Space Ranger pipeline to process 10x spatial transcriptomics data |
| nf-core/spotiflow | imaging image microscopy transcriptomics spatial spot detection | Spotiflow, accurate and efficient spot detection with stereographic flow. |
| nf-core/xeniumranger/import-segmentation | spatial segmentation import segmentation nuclear segmentation cell segmentation xeniumranger imaging | 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. |