Nextflow Modules
Showing module(s) with keyword "imaging"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/basicpy | Process | 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/baysor/run | Process | segmentation spatial transcriptomics cell clustering imaging | Bayesian segmentation of spatial transcriptomics data. |
| nf-core/bftools/showinf | Process | metadata ome-tif ome-tiff imaging bioinformatics tools | Extract OME xml data from OME-tif |
| nf-core/bioformats2raw | Process | 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 | Process | imaging spatial_omics segmentation | Deepcell/mesmer segmentation for whole-cell |
| nf-core/imc2mc | Process | 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 | Process | 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 | Process | 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 | Process | 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 | Process | anndata spatialdata metabolomics mass spectrometry imaging | Export METASPACE datasets to AnnData and SpatialData objects |
| nf-core/mindagap/duplicatefinder | Process | imaging resolve_bioscience spatial_transcriptomics | marks duplicate spots along gridline edges. |
| nf-core/mindagap/mindagap | Process | imaging resolve_bioscience spatial_transcriptomics | Takes a single panorama image and fills the empty grid lines with neighbour-weighted values. |
| nf-core/molkartgarage/clahe | Process | clahe image_processing imaging correction | Contrast-limited adjusted histogram equalization (CLAHE) on single-channel tif images. |
| nf-core/phenoimager2mc | Process | 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/rami2d/register | Process | registration imaging multiplex spatial | offers 3 pre-defined registration schemes 1) Rigid, 2) Rigid+Affine 3) Rigid+Affine+Bsplines, each of them providing more geometrical adaptability and thus more control in the final outcome. |
| nf-core/rami2d/transform | Process | imaging spatialomics multiplexed registration transform | Applies transformations to images using RAMI2D, designed to take the transformation maps produced by rami2d-register |
| nf-core/raw2ometiff | Process | ome tiff imaging | write your description here |
| nf-core/spaceranger/count | Process | align count spatial spaceranger imaging | Module to use the 10x Space Ranger pipeline to process 10x spatial transcriptomics data |
| nf-core/spotiflow | Process |