Constantin Pape - Adventures in Large Scale Image Analysis

I am a PhD student at EMBL Heidelberg and at the University of Heidelberg, working in the groups of Anna Kreshuk and Fred Hamprecht.

I focus on the application of Machine Learning and Computer Vision for analysing large microscopy data, mostly working on image segmentation. This includes scaling algorithms to TB sized datasets, developing new efficient algorithms and adapting algorithms for domain specific problems.

I work in collaboration with several biology groups at EMBL, on topics such as understanding the evolutionary origins of cells in Platynereis and beyond or unraveling the evolution of neural cells in sponges.

The tools I develop are available as open source software:

• cluster_tools: a python library for large scale image analysis on compute clusters
• elf: a python library for convenient large scale image analysis
• z5: a C++ library with python bindings to read and write data in zarr/n5 format

You can also find me here: