The Open Microscopy Environment

openmicroscopy.org

91 points·pabs3··10 comments

If anyone is interested in similar challenges, but in cryo electron microscopy, where the datasets are dozens of TB, this is a good paper discussing the file formats, header organization, and bit-depth required for proper resolution:

https://pubmed.ncbi.nlm.nih.gov/35724904/

What I can say is that TEM data management is unmitigated hell, and thank God for that author (Ludtke) and his software (EMAN2).

Biologists are unsurprisingly awful at data management.

Noob question here, how can I read this paper? Or I need to purchase access?

Use sci-hub

Their data management strategy is organic.

and in the case of the cryo-em researchers, completely frozen.

I reverse engineered several microscopy formats, it can be a lot of fun. If anyone is interested in contributing to similar such efforts there is also https://openslide.org/

Sheesh openslide was an absolute game changer when I was writing code to be able to utilize digital pathology and microscopy data in a browser. They've done some awesome work. I really enjoyed learning about the different formats and can't recommend the resources at OpenSlide enough.

OME is the best organization we have for standards in microscopy, especially bioimaging.

related: I know of 2 open source projects for building a microscope (3D printed):

- openflexure https://openflexure.org/projects/microscope/ - PUMA https://github.com/TadPath/PUMA

These are both extremely impressive projects. I've used an earlier version of the OpenFlexure stage for an unrelated project, and it was a very easy build. Very well thought out.

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