A dozen programmers from around the world got together in early September to join forces in order to develop software called FIJI. The hackathon, a gathering of developers known in the IT community, was initiated by researchers from IT4Innovations, who have been working on a specialized image processing software package for a long time.
Six days, developers from the Czech Republic, France, Germany, Sweden, and the USA, full-time programming, intensive team discussions on how to solve the problems emerged, and many cups of coffee. This is how one could briefly describe the FIJI hackathon, which was held for the third time under the patronage of IT4Innovations, but otherwise as the forty-second one in a row. Just after the summer holidays, the attention of all participants shifted to the FIJI software, which is used to process biological images, such as those from microscopy, images of cells, tissues, and whole organisms, and which for these reasons is primarily used by the broad biological scientific community.
However, the software, popular with scientists, offers further room for improvement, especially in user-friendliness. "We are trying to adapt the software so that users can process their images in parallel, i.e. accelerated on a supercomputer. Because of parallelisation, we need to change the traditional way of storing images into a cluster-friendly format for sharing the whole image and especially parts of it. And that is what we started at the September hackathon. We managed, for the first time in FIJI, to have a user taking their large image stored in a new community format called NGFF or OME.Zarr and view its contents in FIJI. This is the beginning of the journey," says Vladimir Ulman, the initiator of the event, who works at IT4Innovations as a researcher and developer of algorithms for segmenting and tracking cells in digital images.
The Hackathon took place from 5th to 10th September 2022 in Olšanka Hotel in Prague in a hybrid form. The meeting was attended by scientists and developers from several countries and renowned research institutes, such as the European EMBL and the American Janelia campus.
The FIJI Hackathon 2022 took place within the framework of the IT4Innovations National Supercomputing Center – path to exascale project, the main objective of which is to upgrade and modernise the IT4Innovations research infrastructure so as to maintain the current technological level of HPC in the Czech Republic as compared to developed, especially European countries. The project also supports quality research of the wide academic community in the Czech Republic and the expansion of existing research activities at IT4Innovations in the areas of modelling of photonic and spin-photonic structures, design of new progressive materials based on electronic structure calculation, and analysis of biological images using HPC, which includes the organisation of the above-mentioned hackathon.
The hackathon was funded by the OP RDE project entitled IT4Innovations National Supercomputing Center – Path to exascale project ID: CZ.02.1.01/0.0/0.0/16_013/0001791.