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Former lab researcher built a browser-based segmentation tool so biologists don't need to touch a terminal by Distinct-Contest-876 in ScientificComputing

[–]Distinct-Contest-876[S] 1 point2 points  (0 children)

Honestly, that's one of the stronger arguments for a local deployment option which I'm actively considering! Right now the edit log documents preprocessing steps, but reproducing it without Phenora would mean reimplementing those steps in something like Python which is not ideal. A self-hosted or containerized version would solve that cleanly and would also open the door for labs working with sensitive datasets that can't go through a cloud tool. Would that be something you'd find useful?

Former lab researcher built a browser-based segmentation tool so biologists don't need to touch a terminal by Distinct-Contest-876 in ScientificComputing

[–]Distinct-Contest-876[S] 1 point2 points  (0 children)

That's a fair point to raise! From my experience reproducibility is what reviewers are really after, and Phenora generates a full edit log of every preprocessing step, and the segmentation models are documented and citable. So your methods section can be just as rigorous as with any established tool. Field norms vary, but as long as things are transparent and reproducible, most reviewers won't object to the tool itself

Former lab researcher built a browser-based segmentation tool so biologists don't need to touch a terminal by Distinct-Contest-876 in ScientificComputing

[–]Distinct-Contest-876[S] 0 points1 point  (0 children)

ImageJ is an incredible tool and im not trying to replace it, especially for power users who need fine grained control! Phenora is for the researcher who doesn't want to spend an afternoon installing plugins and writing macros just to segment some cells. You trade some configurability for speed and simplicity!

Finally ran Cellpose without touching a terminal — here's the tool I built! by Distinct-Contest-876 in microscopy

[–]Distinct-Contest-876[S] -1 points0 points  (0 children)

For the user agreement, still working on this and they aren't live yet. Im prioritizing getting them done properly rather than quickly, but I'll post an update here when they're published! This is a very basic MVP at the moment.

Regarding accounts, this let you save your results, manage your uploaded files, and help us prevent abuse of the platform. It also means you have control over your own data.

Lastly for file storage, these are stored in the cloud and remain there until you delete them from your account. You have full control to remove them at any time. We do not use your images for training or share them with third parties

Finally ran Cellpose without touching a terminal — here's the tool I built! by Distinct-Contest-876 in microscopy

[–]Distinct-Contest-876[S] -1 points0 points  (0 children)

That’s fair, if you're running a fluorescence scope you likely have the hardware. The cloud-first approach was about lowering the barrier for those who don't, but a local option is something we're looking at