mjseignon

mjseignon's Stars

• facebookresearch/segment-anything

  The repository provides code for running inference with the SegmentAnything Model (SAM), links for downloading the trained model checkpoints, and example notebooks that show how to use the model.

  Language:Jupyter Notebook47.2k3056645.6k

• vega/altair

  Declarative statistical visualization library for Python

  Language:Python9.3k1402k792

• stardist/stardist

  StarDist - Object Detection with Star-convex Shapes

  Language:Python90926227221

• vanvalenlab/deepcell-tf

  Deep Learning Library for Single Cell Analysis

  Language:Python4171627196

• ome/bioformats

  Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment. Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.

  Language:Java38029501241

• hms-dbmi/viv

  Library for multiscale visualization of high-resolution multiplexed bioimaging data on the web. Directly renders Zarr and OME-TIFF.

  Language:JavaScript2821426845

• scverse/spatialdata

  An open and interoperable data framework for spatial omics data

  Language:Python2301037743

• ssadedin/bpipe

  Bpipe - a tool for running and managing bioinformatics pipelines

  Language:Groovy2271825757

• digitalcytometry/ecotyper

  EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.

  Language:R18039742

• labsyspharm/mcmicro

  Multiple-choice microscopy pipeline

  Language:Nextflow1041324558

• seqeralabs/nextflow-tutorial

  Nextflow training material for introductory tutorial

  Language:Nextflow1014045

• BodenmillerGroup/ImcSegmentationPipeline

  A pixel classification based multiplexed image segmentation pipeline

  Language:Jupyter Notebook842211836

• CSOgroup/cellcharter

  A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.

  Language:Python802232

• rnakato/ShortCake

  A docker image for single-cell analysis

  Language:R665813

• nf-core/spatialvi

  Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.

  Language:Nextflow501532918

• BodenmillerGroup/steinbock

  A toolkit for processing multiplexed tissue images

  Language:Python491020815

• vitessce/vitessce-python

  Python API and Jupyter widget for Vitessce

  Language:Python4061727

• AllenCellModeling/napari-aicsimageio

  Multiple file format reading directly into napari using pure Python

  Language:Python3374010

• MaayanLab/appyter-catalog

  A catalog of appyter notebooks

  Language:Jupyter Notebook33512744

• BodenmillerGroup/cytomapper

  R package for visualization of highly multiplexed imaging data

  Language:R3210699

• plevritis-lab/CELESTA

  Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information for multiplexed in situ imaging data. No training dataset with cell type labels is required.

  Language:R27589

• nf-core/imcyto

  Image Mass Cytometry analysis pipeline

  Language:Python25133717

• TheJacksonLaboratory/cs-nf-pipelines

  The Jackson Laboratory Computational Sciences Nextflow based analysis pipelines

  Language:Nextflow205810

• hubmapconsortium/codex-pipeline

  CODEX data processing code

  Language:Python1018344

• BodenmillerGroup/napari-imc

  Imaging Mass Cytometry (IMC) file type support for napari

  Language:Python95303

• SlicerMicro/Slicer-TITAN

  TITAN is responsible for the pre-processing and analysis tasks of imaging mass cytometry (IMC) data. https://doi.org/10.1002/cyto.a.24535

  Language:Python4232

• TheJacksonLaboratory/scbl-utils

  A set of command-line utilities that facilitates data processing in the Single Cell Biology Lab at the Jackson Laboratory.

  Language:Python3190

• ahmed-said-jax/scamplers

  A command-line utility to interact with a MongoDB designed for single cell data processing.

  Language:Rust2200

• muschellij2/bftools

  BioFormats Tools

  Language:R2423

• TheJacksonLaboratory/slurm-templates

  Slurm templates and notes.

  Language:Shell2