CODEX data processing code
☆12Jul 1, 2025Updated 8 months ago
Alternatives and similar repositories for codex-pipeline
Users that are interested in codex-pipeline are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- A pipeline to transform images into valuable analysis items☆18Jun 18, 2025Updated 9 months ago
- Learn morphological states of dynamic cells☆13Apr 16, 2023Updated 2 years ago
- Multiple-choice microscopy pipeline☆149Feb 27, 2026Updated 3 weeks ago
- ☆11Mar 2, 2021Updated 5 years ago
- A pixel classification based multiplexed image segmentation pipeline☆106Dec 5, 2023Updated 2 years ago
- Single Cell Multiplexed Imaging Jupyter Voila Dashboard using CODEX Data☆17Jul 6, 2023Updated 2 years ago
- Unix table column and row manipulation using column names☆11Feb 24, 2026Updated 3 weeks ago
- Image Mass Cytometry analysis pipeline☆26Jun 3, 2025Updated 9 months ago
- R package for visualization of highly multiplexed imaging data☆34May 27, 2025Updated 9 months ago
- Spatial Image Analysis of Tissues☆15Dec 8, 2022Updated 3 years ago
- Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information …☆39May 7, 2024Updated last year
- DeepREAL: A Deep Learning Powered Multi-scale Modeling Framework Towards Predicting Out-of-distribution Receptor Activity of Ligand Bindi…☆11Apr 23, 2022Updated 3 years ago
- ☆11May 16, 2023Updated 2 years ago
- A BaSiC Tool for Background and Shading Correction of Optical Microscopy Images☆65Mar 12, 2025Updated last year
- Microscopy Image Cytometry Toolkit☆114Jul 15, 2022Updated 3 years ago
- native Python dataclasses for the OME data model☆65Feb 12, 2026Updated last month
- Piecewise alignment for layers of mosaics☆41Feb 18, 2026Updated last month
- ☆18Apr 5, 2024Updated last year
- MethodsJ2☆14May 6, 2022Updated 3 years ago
- INSPIRE: Intensity and Spatial Information-Based Deformable Image Registration☆12Jun 30, 2021Updated 4 years ago
- List of academic institutes/companies working on computer-based digital pathology image analysis☆45Aug 7, 2025Updated 7 months ago
- GitHub Action to launch a workflow using Nextflow Tower.☆12Mar 28, 2023Updated 2 years ago
- Source code and data for "Causal reasoning over knowledge graphs leveraging drug-perturbed and disease-specific transcriptomic signatures…☆19Jul 3, 2024Updated last year
- ☆13Sep 18, 2018Updated 7 years ago
- CHAMMI: A benchmark for channel-adaptive models in microscopy imaging☆14Oct 23, 2024Updated last year
- Python API and Jupyter widget for Vitessce☆62Mar 16, 2026Updated last week
- CytoData 2016 – origin story☆18Sep 15, 2017Updated 8 years ago
- ☆11Dec 26, 2017Updated 8 years ago
- Evaluating the quality of a cell segmentation method without reference.☆13Jul 26, 2025Updated 7 months ago
- Spatially-resolved Transcriptomics via Epitope Anchoring☆20Apr 1, 2024Updated last year
- Image registration (alignment) software for large microscopy images☆27Oct 15, 2023Updated 2 years ago
- R package: AutoSpill algorithm for calculating spillover coefficients to compensate or unmix high-parameter flow cytometry data☆20Jun 17, 2021Updated 4 years ago
- Dataset for Natural Focus Blurr Assessment in Digital Pathology☆15Nov 19, 2019Updated 6 years ago
- Image processing software for CODEX: driftcompensation, deconvolution, uploading and segmentation☆52May 20, 2022Updated 3 years ago
- Easily read and write ome-tiff images in python☆28May 6, 2024Updated last year
- Run TFLITE models on the web☆12Jan 2, 2022Updated 4 years ago
- A workflow for redacting PHI from whole slide images (WSI) based on the Digital Slide Archive.☆18Feb 27, 2026Updated 3 weeks ago
- A Python package mapping 2D coordinates to colors based on different 2D color maps.☆16Dec 4, 2025Updated 3 months ago
- Python tools for creating and manipulating OME-TIFF multi-resolution pyramid images.☆18Aug 8, 2025Updated 7 months ago