fish-quant / big-fish-examples
Notebooks to illustrate how BigFISH is working.
☆13Updated 2 years ago
Alternatives and similar repositories for big-fish-examples:
Users that are interested in big-fish-examples are comparing it to the libraries listed below
- Toolbox for the analysis of smFISH images.☆58Updated last year
- Detection, colocalization, and quantification of spots / puncta☆12Updated last year
- Generate HCR-style Probe Pairs for mRNA visualization☆36Updated last year
- Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoC…☆157Updated this week
- Spatial Single-Cell Analysis Toolkit☆83Updated this week
- Bayesian Segmentation of Spatial Transcriptomics Data☆159Updated last month
- Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information …☆31Updated 8 months ago
- Interactive visualization of spatial omics data☆47Updated this week
- CellProfiler tutorial pipelines and images☆86Updated 3 months ago
- a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challe…☆45Updated this week
- Multiple-choice microscopy pipeline☆118Updated this week
- A scalable machine learning pipeline for probe specificity prediction.☆13Updated last year
- An open and interoperable data framework for spatial omics data☆249Updated this week
- Matlab software for the analysis of MERFISH data and the construction of MERFISH probes.☆50Updated 3 years ago
- A pixel classification based multiplexed image segmentation pipeline☆86Updated last year
- Integrated pipeline for multiplexed image analysis☆79Updated 2 months ago
- A self-explanatory, hands-on intro to bioimage analysis in python. Slightly outdated but still much liked by learners.☆97Updated last year
- The 2023 version of cellPLATO☆13Updated 2 months ago
- A Python toolkit for flow cytometry analysis supporting GatingML and FlowJo workspaces☆163Updated 2 weeks ago
- Rapids_singlecell: A GPU-accelerated tool for scRNA analysis. Offers seamless scverse compatibility for efficient single-cell data proces…☆168Updated this week
- ☆68Updated last month
- This repository is used for the HeaDS git and GitHub workshop 2023☆16Updated 3 months ago
- A tool for semi-automatic cell type classification☆330Updated last month
- starfish: unified pipelines for image-based transcriptomics☆230Updated 3 weeks ago
- Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data☆297Updated 5 months ago
- Differential expression analysis for single-cell RNA-seq data.☆195Updated last year
- Scanpy Tutorials.☆196Updated this week
- A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas☆52Updated this week
- A Python GUI-based framework for segmentation, tracking and cell cycle annotations of microscopy data☆143Updated this week
- Deconvolution of widefield microscopy images and generation of point spread functions☆45Updated this week