All the code described in the Lee et al. (2023) paper

Solve Visual Understanding with Reinforced VLMs

Segment Anything for Histopathology

3DCellComposer - A Versatile Pipeline Utilizing 2D Cell Segmentation Methods for 3D Cell Segmentation

PAthological QUpath Obsession - QuPath and Python conversations

Lab for quantitative bioimage analysis experiments in Python

Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many other features.

desktop app (cmd and gui) to repair or merge (boolean and/or) multiple surface/solid meshes

Python library containing utility functions used within BIAFLOWS wrapper files (annotation export, metrics computation).

EDAM is a domain ontology of data analysis and data management in bio- and other sciences, and science-based applications. It comprises concepts related to analysis, modelling, optimisation, and da…

scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images

Interact with workflow tasks in napari

2024 OME-Zarr Hackathon project for benchmarking read performance of chunk sizing on different storage environments

Ontology of bioimage informatics operations, topics, types of data, and data formats. EDAM-Bioimaging is an extension of the EDAM ontology (edamontology.org) dedicated to bioimaging data analysis, …

Interprocess cooperation with shared memory

pathlib api extended to use fsspec backends

Official PyTorch implementation of the "SN2N" -v0.3.5

A single repo of all available/potential tabular normalization methods for downstream analysis of spatial proteomics datasets.

Course and material for the clesperanto workshop presented at I2K 2024

Loading and handling microscopy data in blender

Create web-based OME-Zarr galleries

Spatial Transcriptomics Quantification pipeline for 10x Visium and H&E-stained whole slide images

Nextflow runs monitoring and organisation UI

Single-cell Annotation and Fusion with Adversarial Open-Set Domain Adaptation Reliable for Data Integration