Sharing and reusing biological images

Our databases hold millions of freely available bioimages. Here are some examples of how they have been shared and reused.

Sharing epic light-sheet microscopy images

Dr. Katrín Möller, a post-doctoral researcher at Biomedical Center of the University of Iceland, recently published a paper in eLIFE A role for the centrosome in regulating the rate of neuronal efferocytosis by microglia in vivo. Katrín also deposited the imaging data supporting her publication in the BioImage Archive. You can read more about this in an article by Euro-BioImaging here.

“I was wondering where to store my data when I learned about the BioImage Archive at the BNMI Symposium from Euro-BioImaging project manager Johanna Bischof. It’s great to have a place to put life-sciences microscopy data.”, says Katrín, ““The BioImage Archive really is a fantastic effort. Despite the hard work, I’m really glad I did this. It feels like a big step towards more sustainable science,” .

Helping test algorithms

Sjors Scheres, research leader at MRC Laboratory of Molecular Biology (LMB) and author of RELION, a widely used processing software for electron microscopy, was an early user of EMPIAR, both as submitter and reuser of data.

“EMPIAR is very useful: it provides us with new data to test and develop our algorithms. Relying only on in-house data provides a very limited view but, because EMPIAR contains data from different sources, it allows us a much wider exposure to tune our algorithms.”, explains Scheres. “Not having it would slow us down.”

EMPIAR hosts the data used for RELION tutorials and benchmarks. Scheres was also involved in a EM community map challenge, in which participants downloaded datasets from EMPIAR and processed them using different workflows and software to compare results.

Sharing screening data

Research institutes often find it difficult to store large datasets and make them publicly available. For this reason, Chris Bakal, research team leader at the Institute for Cancer Research, submitted data from his research to IDR.

“We want people to be able to reproduce our research results and re-analyze our data in their own way. For that, it is essential that people have access to the raw data. Databases such as IDR are an easy place to store it”, says Bakal, who deposited both image and quantitative screening data from his research in IDR. “Our research is supported by grants and public funds so it is important that our results are shared with the scientific community.”