Easy Volumetric Segmentation with Deep Learning

Image data format specification for spaceTx

An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.

R package to analyze single cell in-situ sequencing (ISS) data

Your Personal Assistant in Computational Bioimaging.

Python libraries for loading, running and packaging bioimage.io models

Segment Anything for Microscopy

Resources for teaching/preparing to teach bioimage analysis

A napari plugin to process and analyse images with chatGPT!

A basis for a napari plugin for manually correcting cell segmentation in 3D (z, y, x) or 4D (t, z, y, x) (virtual) arrays.

RAxML Next Generation: faster, easier-to-use and more flexible

Padlock design pipeline for multiplexed assay with multiple probes per target in cDNA-based expression profiling

GPU-accelerated general purpose image processing and image analysis in napari

napari: a fast, interactive, multi-dimensional image viewer for python

Registration to BrainGlobe atlases in napari using Elastix

3-day workshop to teach biologists how to train and process deep convolutional neural networks for image segmentation through a comprehensive image analysis pipeline for immune profiling of 2D mult…

Python Jupyter notebooks for BioImageAnalysis, GPU-accelerated image processing, bio-image data science and more

NEUBIAS Academy @Home: Interactive Bioimage Analysis with Python and Jupyter

This is the repository for a Python bioimage analysis course which establishes the fundamentals of image analysis in the context of biological imaging.

Material and Instruction for the course "Bioimage data management and analysis with OMERO"

scikit-image web page generated html

Image processing in Python

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

Tools for Flexible Spectroscopic Inference