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brisvag / blik

Python tool for visualising and interacting with cryo-ET and subtomogram averaging data.
https://brisvag.github.io/blik/
GNU General Public License v3.0
23 stars 8 forks source link

3D interactivity #28

Open alisterburt opened 3 years ago

alisterburt commented 3 years ago

We need to have a working system for 3d interactivity/annotation eventually, ideally on 2d slices visualised in 3D so we can be precise and remove ambiguity

This is an ideal candidate for something that we should develop directly within the napari ecosystem and then use ourselves

alisterburt commented 3 years ago

napari/napari#515 and napari/napari#839 are of interest here

cnstt commented 2 years ago

Hello @alisterburt, I just developed a napari plugin that is capable to visualise cryo-ET data in 3D and that has an orthoslice viewer (3 2d slices: xy, xz and yz). The tool is also capable to annotate and handle all functionalities of DeepFinder https://gitlab.inria.fr/serpico/deep-finder. The plugin is available here: https://github.com/deep-finder/napari-deepfinder. The orthoslice view is not perfect, but as this hasn't been integrated in napari yet, I needed to use some tricks to make it work. I hope this might help you :)

alisterburt commented 2 years ago

@cnstt this is super cool, thanks for sharing!! Would you like to demo this at the napari community meeting next week?! I would love to see it in action, the orthoslice viewer sounds amazing :)

Excited to see more cryo-ET people using napari!!

cnstt commented 2 years ago

@cnstt this is super cool, thanks for sharing!! Would you like to demo this at the napari community meeting next week?! I would love to see it in action, the orthoslice viewer sounds amazing :)

This sounds amazing, thanks a lot! I could definetely demo this at the napari community meeting ;) The software is still in it's early stages (hasn't been published to pip yet), but it is ready for a first demo :)

alisterburt commented 2 years ago

Great! In case you aren't aware we also have napari.zulipchat.com for some synchronous chat, feel free to reach out on there any time!