Nextflow Modules
Showing module(s) with keyword "segmentation"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/baysor/run | Process | segmentation spatial transcriptomics cell clustering imaging | Bayesian segmentation of spatial transcriptomics data. |
| nf-core/cellpose | Process | segmentation image cellpose gpu spatial-transcriptomics | cellpose segments cells in images using GPU-accelerated deep learning |
| nf-core/deepcell/mesmer | Process | imaging spatial_omics segmentation | Deepcell/mesmer segmentation for whole-cell |
| nf-core/ilastik/multicut | Process | multicut segmentation pixel classification | Ilastik is a tool that utilizes machine learning algorithms to classify pixels, segment, track and count cells in images. Ilastik contains a graphical user interface to interactively label pixels. However, this nextflow module will implement the --headless mode, to apply pixel classification using a pre-trained .ilp file on an input image. |
| nf-core/ilastik/pixelclassification | Process | pixel_classification segmentation probability_maps | Ilastik is a tool that utilizes machine learning algorithms to classify pixels, segment, track and count cells in images. Ilastik contains a graphical user interface to interactively label pixels. However, this nextflow module will implement the --headless mode, to apply pixel classification using a pre-trained .ilp file on an input image. |
| nf-core/numorph/3dunet | Process | segmentation cell nuclei light-sheet microscopy numorph | 3DUnet for cell nuclei quantification on 3D microscopy images of the numorph toolkit. |
| nf-core/proseg/proseg | Process | segmentation spatial transcriptomics | Proseg (probabilistic segmentation) is a cell segmentation method for in situ spatial transcriptomics. |
| nf-core/proseg/proseg2baysor | Process | segmentation spatial transcriptomics | Convert proseg outputs to baysor format for import to Xenium explorer |
| nf-core/stardist | Process | stardist segmentation image gpu spatial-transcriptomics | Cell and nuclear segmentation with star-convex shapes |
| nf-core/tiff_segmentation_vpt | Workflow | segmentation imaging merscope vizgen tiff spatial | Perform segmentation of MERSCOPE TIFF images using the vizgen-postprocessing tool |
| nf-core/vizgenpostprocessing/compiletilesegmentation | Process | vpt vizgen segmentation microscopy spatial transcriptomics | The module compiles segmentation tiles using Vizgen's post-processing tool. |
| nf-core/vizgenpostprocessing/preparesegmentation | Process | vpt vizgen segmentation microscopy spatial transcriptomics | The module prepares the specification JSON file for Vizgen's post-processing tool cell segmentation workflow. |
| nf-core/vizgenpostprocessing/runsegmentationontile | Process | vpt vizgen segmentation microscopy spatial transcriptomics | The module runs the segmentation algorithm on a specific tile using Vizgen's post-processing tool. |
| nf-core/xeniumranger/importsegmentation | Process | spatial segmentation import segmentation nuclear segmentation cell segmentation xeniumranger imaging | The xeniumranger importsegmentation 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. |
| nf-core/xeniumranger/resegment | Process | spatial resegment morphology segmentation xeniumranger | The xeniumranger resegment module allows you to generate a new segmentation of the morphology image space by rerunning the Xenium Onboard Analysis (XOA) segmentation algorithms with modified parameters. |