using this plugin with spatial transcriptomic data (from squidpy)

[sophieRAIBAUD]

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

[dstansby]

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]

ok thanks !!
I have 2 question then :)

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

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]

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]

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...

[dstansby]

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!