Nov 14, 2023
Nutil Data Integration
- Michael X. Henderson1
- 1Van Andel Institute
- Michael X. Henderson: ORCHID: 0000-0001-9710-0726
Protocol Citation: Michael X. Henderson 2023. Nutil Data Integration. protocols.io https://dx.doi.org/10.17504/protocols.io.3byl4qrz8vo5/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: August 17, 2023
Last Modified: May 31, 2024
Protocol Integer ID: 90665
Keywords: ASAPCRN
Funders Acknowledgement:
Aligning Science Across Parkinson’s
Grant ID: ASAP-020616
National Institute on Aging
Grant ID: R01-AG077573
Abstract
This protocol describes Nutil data integration from segmentation and registration of mouse brain data.
Attachments
812-2118.pdf
4.6MB
Nutil Data Quantification
Nutil Data Quantification
Open Nutil and find operation tab.
Find the 3 folders you created at the beginning of this workflow and populated during the workflow and populate them into their corresponding list above. (segmentation is your input folder, brain atlas map folder is your atlas folder, output folder is output and should be empty still XML or JSON anchoring file is the QuickN JSON file that you created earlier – you can also use visualign json file it doesn’t matter the anchor is set in quickNII and nonlinear adjustments are made in reference to it. Object color Is black because that’s what the staining of our segmentations look like if it were a different color we would need to look for another object color.
Navigate to advanced settings In the row labeled Global Pixel Scale/Unit, set it to 36.44778384 um2. (6.0 is new value for van andel scans) The NEW images that are scanned here at Van Andel are resolved at 0.5031 microns per pixel, so if we downsized by 12 we get 6.0372 then this number is squared to account for um2. the final value is 36.44778384.
Also, under advance settings change custom masking to yes and select the color of the hemisphere of interest i.e. white to view hemisphere masked in white mask. Also select the folder location of the mask. Repeat the color selection with black to view the other hemisphere masked by black.