BIOP / biop-bash-scriptsLinks
Bash scripts to simplify your life (let's hope so!)
☆11Updated 3 months ago
Alternatives and similar repositories for biop-bash-scripts
Users that are interested in biop-bash-scripts are comparing it to the libraries listed below
Sorting:
- Piecewise alignment for layers of mosaics☆29Updated last month
- QuPath extension for Cellsparse☆19Updated 5 months ago
- The official QuPath extension for InstanSeg☆27Updated last week
- QuPath extension to interactively align images☆25Updated 2 months ago
- ☆28Updated this week
- Part 1 of Allen Cell and Structure Segmenter: classic image segmentation workflow☆26Updated last year
- 3D segmentation for cells and organoids of 3D multichannel images☆24Updated 4 months ago
- TissUUmaps is a browser-based tool for fast visualization and exploration of millions of data points overlaying a tissue sample. TissUUma…☆63Updated 5 months ago
- ☆34Updated last year
- Raw format to OME-TIFF converter☆56Updated last month
- Development of PICASSO plugin for napari☆16Updated 2 years ago
- EASI-FISH analysis pipeline for spatial transcriptomics☆35Updated 11 months ago
- Evaluating the quality of a cell segmentation method without reference.☆12Updated 3 months ago
- Spatial Transcriptomics Quantification pipeline for 10x Visium and H&E-stained whole slide images☆21Updated 5 months ago
- QuST: QuPath Extension for Integrative Whole Slide Image and Spatial Transcriptomics Analysis☆32Updated 4 months ago
- Interactive visualization of spatial omics data☆70Updated last week
- ☆32Updated 3 months ago
- A visualization app for 3D-registered data processed in ABBA and QuPath☆20Updated 3 years ago
- multimodal whole slide image registration in a graph structure☆95Updated last year
- Tools and scripts for EASI-FISH image data analysis☆17Updated 3 years ago
- Integrated pipeline for multiplexed image analysis☆98Updated 7 months ago
- Bio-Formats image file format to raw format converter☆100Updated last month
- An Interactive Image Segmentation Filter for Multiplex Microscopy☆31Updated last month
- Generate consensus 3D cells segmentations by combining 2D cell segmentations from any combination of xy, xz, yz views, compatible with ou…☆22Updated 2 months ago
- CODEX data processing code☆12Updated 3 months ago
- Biologically-informed deep learning for cell segmentation of subcelluar spatial transcriptomics data☆45Updated last year
- Aligning images acquired with the IBEX microscopy imaging technique☆18Updated this week
- A Python-based tool for parallelized conversion of image datasets from various formats to OME-Zarr, with support for distributed processi…☆12Updated last week
- Image registration (alignment) software for large microscopy images☆25Updated 2 years ago
- ☆24Updated 2 years ago