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matplotlib / napari-matplotlib

Linking napari layers with Matplotlib plots
https://napari-matplotlib.github.io/
BSD 3-Clause "New" or "Revised" License
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using this plugin with spatial transcriptomic data (from squidpy) #55

Closed sophieRAIBAUD closed 1 year ago

sophieRAIBAUD commented 2 years ago

Hello This matplotlib pluggin is great but it doesnt seam to work on my spatial transcriptomic data .... I launched it with squidpy Many thanks Sophie image

dstansby commented 2 years ago

It looks like you have a points layer selected on the left - the slice widget will only work with image layers, so if you click the hires layer hopefully it works? We should definitely add a helpful messgage in the widget that says to select an Image layer though, so thanks for reporting this!

sophieRAIBAUD commented 2 years ago

ok thanks !! I have 2 question then :)

  1. this slice seams to work (y axis = 0 ?) image this one is very strange (values of x between 0 and 2...) image

  2. would you consider to work on spatial transcriptomic data ? on the pont data I have is a gene whose expression was measured in each dot

many many thanks ! Sophie

dstansby commented 1 year ago

Could you eplain a bit more why the second image is a bit strange? It looks the same as the first image to me.

would you consider to work on spatial transcriptomic data ?

napari-matplotlib is meant to be a very broad and generic package, so it won't include any research area specific features. If there are any generic features you are insterested in adding suggestions would be super welcome!

sophieRAIBAUD commented 1 year ago

working on spatial transcriptomic data would be great. There is a plugin for napari by squipy team what I woul like to have is extraction og genes expression under 1 spot... image

dstansby commented 1 year ago

I think this is out of scope for napari-matplotlib, as it is designed to have generic tools that can be used on any data types - thanks for opening though!