Stars
A Python toolbox for registering / fusing / stitching large multi-view / multi-positioning image datasets in 2-3D.
Codebase for "A Foundation Model for Cell Segmentation"
An introduction to OME-Zarr for big bioimaging data
TissUUmaps is a browser-based tool for fast visualization and exploration of millions of data points overlaying a tissue sample. TissUUmaps can be used as a web service or locally in your computer,…
Repo for the Complete Agentic AI Engineering Course
Rembg is a tool to remove images background
nnInteractive plugin for Napari - nnInteractive is a framework for 3D interactive segmentation, supporting intuitive prompts like points, scribbles, bounding boxes, and lasso. Trained on 120+ diver…
Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / etc)
A plugin to quickly generate ground truth with sparse labels
Open source Python library for building bioimage analysis pipelines
This is the supplementary code for Dark sectioning. And it is private now
Probabilistic cell segmentation for in situ spatial transcriptomics
Trainable 2D projection of 3D microscopy stacks using deep learning
outlook-bob is an LLM-based assistant for answering emails. It uses local LLMs using ollama for optimal privacy.
An ImageJ/Fiji plugin designed to effortlessly integrate Segment-Anything models (SAMs) without code.
We developed a python UI based on labelme and segment-anything for pixel-level annotation. It support multiple masks generation by SAM(box/point prompt), efficient polygon modification and category…
Stitching of large tiled datasets
collection of mass spectrometry imaging workflows
Code for my personal page - made with RStudio/Quarto
starfish: unified pipelines for image-based transcriptomics
Ngio is a Python library to streamline OME-Zarr image analysis workflows.
Nanoscopy library for Python (NanoPyx, the successor to NanoJ) - focused on light microscopy and super-resolution imaging
A python package and graphical user interface to perform single-cell analysis for two interacting populations on multimodal time lapse microscopy images.
A napari plugin for direct 3D cell segmentation -- taking you through training, inference, and review of masks