Mar 31, 2020
Image Registration of MALDI IMS to Microscopy
- 1Vanderbilt University
Protocol Citation: Nathan Heath Patterson, Elizabeth Neumann, Jamie Allen, Danielle Gutierrez, Jeff Spraggins 2020. Image Registration of MALDI IMS to Microscopy. protocols.io https://dx.doi.org/10.17504/protocols.io.bed2ja8e
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: March 31, 2020
Last Modified: October 18, 2023
Protocol Integer ID: 34970
Keywords: HuBMAP, BIOMIC, Vanderbilt, Multimodal Imaging, IMS, Image Registration
Abstract
Scope:
To process to register MALDI IMS images to different types of microscopy images.
Generate a MALDI imaging mass spectrometry (IMS) pixel map using regToolboxMSRC
https://github.com/nhpatterson/regtoolboxmsrc
Using FIJI ImageJ, select corresponding laser ablation marks and IMS pixels in the post-acquisition autofluorescence (post-AF) and IMS pixel map, respectively.
https://fiji.sc
Use a "Landmark Correspondences" FIJI plugin to find an affine transformation between the two images, resampling the post-AF image to the IMS pixel map by selecting post-AF image as source image, and IMS pixel map as the template image within the plugin.
Save the post-AF image.
Using regToolboxMSRC again, align other microscopy modalities (pre-IMS acquisition autofluorescence, brightfield PAS, multiplex immunofluorescence) to the newly saved post-AF image.
When complete, all images will be sampled in the same coordinates as the IMS pixel map.