Code for the article In toto imaging and reconstruction of post-implantation mouse development at the single-cell level

Simple devices and software to facilitate microscopy, electrophysiology, and microbiology techniques for systems neuroscience research. Easy to fabricate and use with low-cost 3D Printers.

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

This is the repository for an image-processing focussed self-taught course with a slight focus on bioimage analysis.

MRI ImageJ related python (jython) module.

PhD dissertation: Methods for Automated Neuron Image Analysis candidate: Miroslav Radojevic Publisher: Erasmus University ISBN 978-94-6361-204-3

A Matlab pipeline for spatiotemporal quantification of monolayer cell migration. The repository includes Matlab source code. This repository is part of the book series "Neubias Bioimage Analysis". The analysis pipeline includes segmentation, velocity measurements, kymographs and multi-dimensional representations and PCA of wound healing assays.

Some CellProfiler plugins.

Hackday project

The IPython notebook contains the questions as well as the related code. Only numpy has been used.

AI-based pathology predicts origins for cancers of unknown primary - Nature

Visualise pcnaDeep single-cell tracking data

cialab/DeepSlides fork to make it work with newer Python libraries.

CaMOS, a GUI for analysis of multimodal neuroscience datasets.

Extraction and tracking of dynamic biopolymer networks.

Source code and workflow protocols for SOCR 3D Cell Morphometry Project

Collection of useful (to me) python scripts for interacting with napari