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alisterburt / napari-mrcfile-reader

Read MRC format image files into napari using the mrcfile package from CCP-EM
BSD 3-Clause "New" or "Revised" License
18 stars 5 forks source link

Writing functions and more #3

Open the-lay opened 3 years ago

the-lay commented 3 years ago

Thanks for merging my previous tiny contribution ("permissive=True")! :)

I want to add writing functions (napari_get_writer, napari_write_image) to the plugin, as well as a dock widget with volume and/or slice histograms. The plugin name however is mrcfile-READER so I don't know whether you see it as an appropriate addition or whether it's out of scope and you'd prefer me to make a new separate plugin. Please let me know your thoughts.

alisterburt commented 3 years ago

@the-lay pleasure! great to work with you 🙂

@Croxa was interested in similar functionality and actually wrote a separate plugin to do it, I suggested combining efforts but haven't yet heard back - what do you think about the idea of us combining efforts and putting together a napari-mrcfile package which wraps useful functionality from mrcfile more completely?

I don't mind where this package lives so if it's useful for you to be able to point to it as a work output it could live on your github

As an aside, it's great to see someone else doing cryo-ET using napari! If you'd like to get a bit more involved, discuss your use case and how we can make napari better for your work definitely hop onto https://napari.zulipchat.com, we'd love to hear about what you're up to!

alisterburt commented 3 years ago

Also, super supportive of the volume/slice histograms in general! I think these should probably be separate from the mrcfile functionality though and live in a standalone plugin before eventually being moved up into napari proper

@haesleinhuepf demoed some really cool histogramming widgets in a napari community meeting recently, maybe we could leverage this to get most/all the way for the functionality you want? I don't think I'll be able to make the meeting this week but it would be great to chat about this stuff live sometime!

philipp-schoennenbeck commented 3 years ago

Hm, I thought I answered you in an e-mail but apparently it did not work. I will gladly work with you on the mrcfile plugin if you want.

alisterburt commented 3 years ago

@Croxa oh cool, looks like we've hit critical mass! 🥳 Same info as I gave to @the-lay applies to you, we'd love to hear about what you're up to at a meeting sometime soon!

Maybe if we jump onto the zulip we can hash out exactly features we want and get a repo together? should be fairly quick now that the ball is rolling!

the-lay commented 2 years ago

Ah I completely missed napari-mrcfile_handler plugin, it does seem that the immediate features I was thinking about are already implemented. I guess then @Croxa 's repository should be the main one since it's already ahead. Regarding renaming, I'd also prefer a cleaner napari-mrcfile than mrcfile-reader or mrcfile_handler. But ultimately I did not contribute to either one and don't want to hijack your projects so I'd be happy with anything you and @Croxa decide.

I also didn't realize the scale of the napari project, very cool! I've signed up on Zulip and would be glad to contribute, but not sure if there's anything more to my usecase than just inspecting .mrc tomograms and segmentations, at least right now.

Also, super supportive of the volume/slice histograms in general! I think these should probably be separate from the mrcfile functionality though and live in a standalone plugin before eventually being moved up into napari proper

Fully agree and yes, it seems to be something that should be provided by napari directly.

alisterburt commented 2 years ago

@the-lay @Croxa cool - let's get a repo set up for napari-mrcfile and get things rolling, I can make one early next week and add you both as collaborators, will be fun 🙂

I'll contact you both on Zulip too! @Croxa I had a quick look but can't see you there, if you have an account could you drop me a message?