scverse / scverse/squidpy

Working on 3D segmentation matrix

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#861 2 comments 0 reactions 1 assignee View on GitHub

@giovp is already working on this.

Since Jul 29, 2024.

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Description

Hello everyone,
First of all, I'd like to extend my sincere thanks to all the developers and contributors to Squidpy and the entire Scanpy ecosystem. Your work is immensely valuable and greatly appreciated.
I've been working with single-cell data for quite a while, but this is my first time exploring spatial data. Following the tutorial on the website, I was analyzing Nanostring data and encountered an issue at the visualization step using sq.pl.spatial_segment. The error message I received was:
ValueError: all the input arrays must have same number of dimensions, but the array at index 0 has 4 dimension(s) and the array at index 1 has 3 dimension(s).
After inspecting my data object and comparing it with the one from the tutorial, I noticed that the "segment" field in my object contains 3-dimensional arrays, whereas the tutorial's object uses 2-dimensional arrays.
Could anyone provide guidance on how I might resolve this issue and successfully visualize my images?
Thank you in advance for your assistance and for fostering such a supportive community.
Best regards!

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