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jni / skan

Python module to analyse skeleton (thin object) images
https://skeleton-analysis.org
BSD 3-Clause "New" or "Revised" License
113 stars 38 forks source link

Example datasets for documentation pages #154

Open jni opened 2 years ago

jni commented 2 years ago
EdwinHernandezG commented 2 years ago

Maybe vessels on 3D? I can share some of those.

jni commented 2 years ago

Thanks @EdwinHernandezG! That would be awesome. If you can put one on Figshare/Dryad/similar with CC-BY or more permissive license, we can add it to the 3D display page! :tada:

jni commented 1 year ago

@EdwinHernandezG how do you feel about sharing one of your vessels datasets for this? 😊

EdwinHernandezG commented 1 year ago

I forgot this, sorry. I am uploading it now to Zenodo. It Is pretty big (24.1 GB). I will write the link as soon as it finishes the upload.

jni commented 1 year ago

It Is pretty big (24.1 GB).

Holy moly! 😂 I think this is too big for building our docs, but will be valuable for napari demos and such, =) so please don't interrupt the upload. Do you think a 2x downscale along each axis, followed by a crop, would be doable? And then uploaded as a separate derived dataset. If we can get under 1GB then that becomes reasonable to process and use in the automated docs build.

EdwinHernandezG commented 1 year ago

So, here It is raw. https://doi.org/10.5281/zenodo.7585093 I will fit iso resolution and generate a pyramidal scheme to see what works best. I have been short of time in the last weeks, but I will find some time to process it.

ns-rse commented 11 months ago

We'd be happy to contribute Atomic Force Microscopy images of DNA and documentation to show how to work with them. I've started work on this and documented progress in an issue that arose in early development #206 (see also earlier references to pruning #97 and #118).

The larger minicircle.spm that we have is available in TopoStats, flattened images ready to analyse look like...