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This repository contains various scripts for automation (mostly for Linux)

Training material based on Carpentries curriculum Building Better Research Software

Batch processing of slide scanner data: How we process (semi-)automatically Zeiss AxioScan Z1 data presented on the Bio-Optics meeting 2025 at Boku.

Integrated Python pipeline to process arbitrary-size .czi files

A Quarto book to document brain registration methods and tools.

A test application for controlling a Fluigent Aria (https://www.fluigent.com/de/forschung/instrumente/aria/) device under NIS Elements macro. A python TCP listens NIS macros to remote control the Aria system using the Fluigent's SDK (https://github.com/Fluigent/aria-sdk).

Mitotic Index from Neural Tube Organoids

1-day long course and hands-on session for image analysis and ImageJ fundamentals.

A fun analysis of the voting results of the IOF Image Competition 2025 that ran on the Open Campus Day 2025.

A seminar on FAIR principles, scientific image processing, and proper figure preparation.