image-analysis-workflows

Segment Source Distribution

ImageJ macros and scripts written at the imaging facility MRI

SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.

I/O operations for OME-TIFF files in Julia

A unified framework for example-based texture synthesis, developed alongside my master's thesis.

An open-source Python framework created for accelerating development of large image analysis workflows

A set of ImageJ plugins to quantify dynamics, morphology, and fluorescence of microglial cells.

Matlab functions to support analysis of digital pathology images.

A local agent architecture for semantic-aware interaction between large language models and multidimensional microscopy datasets inside napari

The material for the Quantitative Big Imaging Course at ETHZ for Spring Semester 2017

Python3 package to analyse GPSeq images and manage TIFF files.

A modular and interactive spatial proteomic image analysis workflow with individual containerized steps, consisting of cell segmentation, unsupervised clustering with optional batch correction, validation of clusters on the image, and cell type clustering results visualization

A 3D Slicer extension for interactive 3D visualization and quantitative colocalization analysis of multi-channel confocal z-stack images.

Toolbox for image analysis pipeline (image pre-processing, feature extraction, feature preprocessing, dimensionality reduction, classification, clustering and regression). Powered by sklearn and other python libraries.

Pipeline for high-throughput analysis of RFP/GFP ratios in vacuoles

Example of how to integrate MATLAB apps into a Python deep learning workflow for computer vision and image analysis tasks.

An open-source image analysis pipeline for single-cell mRNA puncta quantification and colocalization.

We build upon Logistic Regression concepts and create a Deep Learning Convolution Neural Network. This repository explains how Logistic Regression is really the root of building Multilayer Perceptron models for Machine Learning and Deep Learning.

MCP tools for Cellpose and napari integration