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).

This is series of protocols that has been adapted from published and unpublished protocols broadly referred to as the QUINT workflow.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).

VisuAlign, RRID:SCR_017978

1. QuPath: http://qupath.github.io/

2. QuickNII: http://www.nitrc.org/projects/quicknii (SELECT ABA Mouse Edition)

3. Visualign: http://www.nitrc.org/projects/visualign/

4. Qmask: \pn.vai.org\projects_secondary\henderson\NOAH\QMask-Standalone

5. Nutil: http://www.nitrc.org/projects/nutil/

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