angelolab / angelolab/maldi-tools

Automatic generation of input masks for MALDI acqusition

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#13 0 則留言 0 個 reaction 已指派 2 人 已被 @alex-l-kong 認領 在 GitHub 檢視
enhancement
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Python
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描述

**Is your feature request related to a problem? Please describe.**
The current MALDI image acquisition pipeline requires the user to manually define the boundaries of each individual FOV. The built-in magic wand tool that Bruker provides is not accurate enough to avoid debris in the image, and fails to automatically identify the majority of TMA cores. This means the user has to individually circle the outline of each TMA core.

**Describe the solution you'd like**
An image processing pipeline that can do a better job at identifying the shape of each TMA core. This pipeline would provide the proposed FOV masks to the Bruker instrument, which would read them in, and allow the user to use these to guide image acquisition.

The acquisition is done based off a scanned version of the slide. The user must coregister (or "teach", as Vivian puts it) the laser with the optical image. It's not clear how this coregistration is stored internally. We would need to account for this when generating our own mask. This is what one of those images looks like:
image

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