applied-systems-biology / jipipeLinks
Java Image Processing Pipeline (JIPipe) is a graphical batch processing language for the ImageJ ecosystem
☆17Updated last month
Alternatives and similar repositories for jipipe
Users that are interested in jipipe are comparing it to the libraries listed below
Sorting:
- Transform CellProfiler and DeepProfiler data for processing image-based profiling readouts with Pycytominer and other Cytomining tools.☆14Updated this week
- ☆15Updated 10 months ago
- WebGL-based viewer for spatially-resolved transcriptomics data☆28Updated 2 years ago
- ☆12Updated 10 months ago
- An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.☆19Updated last week
- script + metadata = standalone component☆42Updated this week
- iFISH Probe Design: a Python3 package to build iFISH probes.☆12Updated 3 years ago
- IHC-image analysis workflow☆23Updated 7 years ago
- ☆29Updated last year
- Graph-based Decoding for In Situ Sequencing☆10Updated 5 years ago
- ☆54Updated this week
- Develop custom oligo design pipelines.☆20Updated last week
- Analyzing cellular niches in spatial transcriptomics data☆29Updated 8 months ago
- Optimal gating strategies for flow and mass cytometry.☆13Updated 3 months ago
- Download and Convert METASPACE datasets to common formats such as AnnData or SpatialData☆11Updated last year
- Spatial Transcriptomics Dashboard☆27Updated 2 years ago
- Minimum Information about Tissue Imaging☆20Updated last year
- TissUUmaps is a browser-based tool for fast visualization and exploration of millions of data points overlaying a tissue sample. TissUUma…☆22Updated 2 years ago
- A plugin to visualise 3D spatial single cell omics☆22Updated last month
- https://sparrow-pipeline.readthedocs.io/en/latest/☆29Updated last month
- Framework for image and flow cytometry analysis☆27Updated 2 months ago
- A Python library for reading and writing Flow Cytometry Standard (FCS) files☆48Updated 2 months ago
- scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images☆47Updated this week
- GRiNCH: Graph-Regularized NMF and Clustering for Hi-C☆9Updated last year
- SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.☆38Updated 2 years ago
- Efficient data structures and IO for whole slide image analysis☆14Updated 3 weeks ago
- Analytical R Tools for Mass Spectrometry☆14Updated 2 years ago
- ☆13Updated last year
- A Python package for gene network analysis☆32Updated 3 years ago
- Build contrasts for models defined with formulaic☆13Updated last week