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The Open Microscopy Environment
- poulpy123 4y agorelated: I know of 2 open source projects for building a microscope (3D printed): - openflexure https://openflexure.org/projects/microscope/ https://openflexure.org/projects/microscope/ - PUMA https://github.com/TadPath/PUMA https://github.com/TadPath/PUMA
- regularfry 4y agoThese 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.
- markkitti 4y agoOME is the best organization we have for standards in microscopy, especially bioimaging.
- mrtweetyhack 4y ago[dead]
- 6451937099 4y ago[dead]
- 6451937099 4y ago[dead]
- ngneer 4y agoI 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/ https://openslide.org/
- randomh3r0 4y agoSheesh 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.
- COGlory 4y agoIf 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/ 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 4y agoTheir data management strategy is organic.
- dekhn 4y agoand in the case of the cryo-em researchers, completely frozen.
- 0xcoffee 4y agoNoob question here, how can I read this paper? Or I need to purchase access?
- cinntaile 4y agoUse sci-hub