Jupyter lab tutorial

On May 5 & 6 2021, I took part in the Workshop “Kompetenz Forschungsdatenmanagement” organized by the Max Planck Digital Library. Day 2 featured a full session on “Reproducible Science with Jupyter” with a presentation by Hans Fangohr (slides available here) followed by an interactive hands-on tutorial. In part 1 of the tutorial, I step through a data analysis workflow based on the Johns-Hopkins University CoViD19 dataset from github. Part 2 and 3 are about Bayesian Inference of SIR model parameters, kindly provided by Johannes Zierenberg from MPI Dynamics and Selforganization. [Read More]

Omero bulk annotation

Edit May 21 2021 I made a short video presentation on the subject, as a “flash” talk for the OME Community Meeting 2021: https://youtu.be/inGQXtbzoZI . Summary This tutorial gives a step-by-step instruction on annotating containers (Projects, Datasets, Plates, or Screens) and individual or multiple images. In particular, we show how to annotate selected images in batch mode using spreadsheet documents as a convenient method to record metadata during or after an experiment. [Read More]