Explore projects

Microscopy Pipeline Constructor (MyPiC)

Course materials for image analysis with the scientific Python stack (numpy/scipy/scikit-image/matplotlib)

Nextflow workflow to convert pyramidal images in PerkinElmer qptiff format to ome-tiff.

Originated from https://github.com/rackt/redux/tree/master/examples/real-world adjusted to work with embase-ng-dev

Recognize different cell types based on morphology features

Tools for online image analysis of images acquired with Zeiss confocal microscopes.

Materials for the ALMF/Bio-IT Image Analysis with Python series, running Spring/Summer 2018

pages at https://grp-bio-it-workshops.embl-community.io/intermediate-python

In this project, we investigated drug impact on gut bacteria by analyzing a large untergeted metabolomics data set and integrating drug-protein interaction networks from STITCH.

Rendered at: https://grp-bio-it.embl-community.io/template-jupyter-book