License: This is an open access collection 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
This collection of protocols was written in the Henderson lab, but all software and original protocols were developed and are available through the NeuroImaging Tools and Resources Collaboratory (NITRC).
Abstract
This is series of protocols that has been adapted from published and unpublished protocols broadly referred to as the QUINT workflow. Note that the original QUINT workflow was generated by Yates and colleagues, and all credit for development of these programs goes to that team. References for each software is listed below.
Yates, S. C. et al. QUINT: Workflow for Quantification and Spatial Analysis of Features in Histological Images From Rodent Brain. Frontiers in neuroinformatics 13, 75, doi:10.3389/fninf.2019.00075 (2019).
Puchades, M. A., Csucs, G., Ledergerber, D., Leergaard, T. B. & Bjaalie, J. G. Spatial registration of serial microscopic brain images to three-dimensional reference atlases with the QuickNII tool. PloS one 14, e0216796, doi:10.1371/journal.pone.0216796 (2019).
The purpose of this workflow is to enable mouse brain segmentation, registration and quantification of regional signal. The simplest segmentation is done in QuPath because this program handles whole slide images and has good segmentation algorithms. Registration is done using 3 programs: QuickNII (aligns to a 3D atlas, typically the 2017 CCFv3 Allen Brain Atlas), Visualign (allows for non-linear warp transformation of the atlas to match sections), QMask (masks each side of the brain to allow for bilateral assessment of brain regions). Segmentations and registrations are then brought together in Nutil, enabling the generation of quantitative measures for every region of the brain.
The programs for registration and quantification rely on having exact file paths from which to call the data. Therefore, it is easiest to set these folders up from the beginning. We have the following typical layout for folders:
1. Project (e.g. Tau-MLi-2)
a. Figure (e.g. Figure 23)
i. Repeat (e.g. 1 or 2)
1. Cohort/Block (e.g. TM1)
a. QuPath (place for qupath project and exported
b. QVN (for QuickNII, Visualign, Nutil)
i. Atlas
ii. Input
iii. Mask
iv. Output_Left
v. Output_Right
b. Figure (next one, same internal folder organization)…
This collection of protocols was written in the Henderson lab, but all software and original protocols were developed and are available through the NeuroImaging Tools and Resources Collaboratory (NITRC).
Yates SC, Groeneboom NE, Coello C, Lichtenthaler SF, Kuhn PH, Demuth HU, Hartlage-Rübsamen M, Roßner S, Leergaard T, Kreshuk A, Puchades MA, Bjaalie JG. QUINT: Workflow for Quantification and Spatial Analysis of Features in Histological Images From Rodent Brain. Front Neuroinform. 2019 Dec 3;13:75. doi: 10.3389/fninf.2019.00075. PMID: 31849633; PMCID: PMC6901597.
Groeneboom NE, Yates SC, Puchades MA, Bjaalie JG. Nutil: A Pre- and Post-processing Toolbox for Histological Rodent Brain Section Images. Front Neuroinform. 2020 Aug 21;14:37. doi: 10.3389/fninf.2020.00037. PMID: 32973479; PMCID: PMC7472695.
Puchades MA, Csucs G, Ledergerber D, Leergaard TB, Bjaalie JG. Spatial registration of serial microscopic brain images to three-dimensional reference atlases with the QuickNII tool. PLoS One. 2019 May 29;14(5):e0216796. doi: 10.1371/journal.pone.0216796.
