The Open Microscopy Environment

[pabs3]

https://www.openmicroscopy.org/

[COGlory]

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.

[nickpeterson → COGlory]

Their data management strategy is organic.

[dekhn → nickpeterson]

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

[0xcoffee → COGlory]

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

[cinntaile → 0xcoffee]

Use sci-hub

[ngneer]

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/

[randomh3r0 → ngneer]

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.

[markkitti]

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

[poulpy123]

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

[regularfry → poulpy123]

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.