Apr 07, 2023

Public workspaceImage Registration of MALDI IMS to Microscopy

 Forked from Image Registration of MALDI IMS to Microscopy
DOI
https://dx.doi.org/10.17504/protocols.io.5qpvor6xxv4o/v1
  • Nathan Heath Patterson1,
  • Jamie Allen1,
  • Angela Kruse1,
  • allison.b.esselman 1,
  • ellie.l.pingry 1,
  • Danielle Gutierrez1,
  • Jeff Spraggins1
  • 1Vanderbilt University
  • VU Biomolecular Multimodal Imaging Center / Spraggins Research Group
  • Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Angela R.S. Kruse
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DOI: https://dx.doi.org/10.17504/protocols.io.5qpvor6xxv4o/v1
Protocol Citation: Nathan Heath Patterson, Jamie Allen, Angela Kruse, allison.b.esselman , ellie.l.pingry , Danielle Gutierrez, Jeff Spraggins 2023. Image Registration of MALDI IMS to Microscopy. protocols.io https://dx.doi.org/10.17504/protocols.io.5qpvor6xxv4o/v1
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: April 05, 2023
Last Modified: October 18, 2023
Protocol Integer ID: 80064
Keywords: HuBMAP, BIOMIC, Vanderbilt, Multimodal Imaging, IMS, Image Registration, image registration of maldi im, maldi ims images to different type, microscopy image, maldi ims image, image registration, microscopy scope, using ims microlink, ims microlink, maldi im, using im, im
Abstract
Scope:
To process to register MALDI IMS images to different types of microscopy images using IMS MicroLink and WSIREG.
Troubleshooting
Install Napari with IMS MicroLink plugin using https://github.com/NHPatterson/napari-imsmicrolink
Use MicroLink to align laser ablation marks from the post autofluorescence image to the IMS pixel map.
Install the WSIREG plugin with Napari https://github.com/NHPatterson/wsireg
Use WsiReg to align other microscopy modalities. These modalities are aligned to the post autofluorescence image.
When complete, all images will be sampled in the same coordinates as the IMS pixel map.