scverse / scverse/spatialdata-io

API for reading in raw MCD files from IMC experiments

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Python
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Description

In the documentation for this package it states that Steinbock outputs from IMC image analysis can be read in through the API. I am wondering if there is a similar function for importing raw MCD files from IMC experiments into a spatialdata object i.e. being able to import raw IMC images without needing to pre-process them through a pipeline and perform downstream analyses such as segmentation and quantification.

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Research direction

The issue names no implementation file or test. Start by reading the documentation statement about Steinbock outputs and the existing API, then determine the supported path for importing raw MCD files into a spatialdata object. Done means raw IMC images can be imported without preprocessing through a pipeline and used for downstream segmentation and quantification.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
bioinformatics
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
30/100

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