BRAINSPACE

This repository contains scripts and files relating to the BRAINSPACE project for the analysis of data from the QUINT workflow. The scripts were used to analyse the data described in the BRAINSPACE article and publicly shared in the EBRAINS repository.

More information on the BRAINSPACE project.

More information on the QUINT workflow.

Overview of files

1. The Nutil_Validation folder contains two test datasets that were used to validate Nutil Quantifier v0.7.0 for the BRAINSPACE project. The test datasets have objects of known size and anatomical location. They were analysed with Nutil Quantifier with the parameters specified in the NutilFileExample.nut file. For both datasets, the results from the Nutil software matched the ground truth for the dataset. The Nutil software has also been validated with other datasets and parameters as described in the user documentation.

2. The Scripts folder contains R scripts that were used to analyse the data in the BRAINSPACE article. See the Wiki for more information of the input, output and purpose of each script.

3. The Intermediate_hierarchy.txt lists the customized regions used for QUINT analysis in the BRAINSPACE project. Each customized region is comprised of regions from the Allen Mouse Brain Atlas Common Coordinate Framework v3 (CCFv3). The assigned custom region name is listed in row 1, with atlas IDs assigned to this region listed below.

4. The SupplementaryTables folder contains supplementary tables for the BRAINSPACE article.

How to cite

BRAINSPACE article

Gurdon B, Yates SC, Csucs G, Groeneboom NE, Hadad N, Telpoukhovskaia M, Ouellette A, Ouellette T, O’Connell K, Singh S, Murdy M, Merchant E, Bjerke I, Kleven H, Schlegel U, Puchades MA, Leergaard TB, Bjaalie JG, and Kaczorowski CC. Detecting the effect of genetic diversity on brain composition in an Alzheimer’s disease mouse model. BioRxiv Preprint. https://doi.org/10.1101/2023.02.27.530226

QUINT workflow

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. https://doi.org/10.3389/fninf.2019.00075.

QuickNII (RRID:SCR_016854)

Puchades MA, Csucs G, Lederberger D, Leergaard TB and Bjaalie JG. Spatial registration of serial microscopic brain images to three-dimensional reference atlases with the QuickNII tool. PLosONE, 2019, 14(5): e0216796. https://doi.org/10.1371/journal.pone.0216796

VisuAlign (RRID:SCR_017978)

Gurdon B, Yates SC, et al. Detecting the effect of genetic diversity on brain-wide cellular and pathological changes in a novel Alzheimer’s disease mouse model. Manuscript in preparation.

ilastik

Berg S., Kutra D., Kroeger T., Straehle C.N., Kausler B.X., Haubold C., et al. (2019) ilastik:interactive machine learning for (bio) image analysis. Nat Methods. 16, 1226–1232. https://doi.org/10.1038/s41592-019-0582-9

Nutil (RRID: SCR_017183)

Groeneboom NE, Yates SC, Puchades MA and Bjaalie JG. Nutil: A Pre- and Post-processing Toolbox for Histological Rodent Brain Section Images. Front. Neuroinform. 2020,14:37. https://doi.org/10.3389/fninf.2020.00037

QCAlign (RRID:SCR_023088)

Gurdon B, Yates SC, et al. Detecting the effect of genetic diversity on brain-wide cellular and pathological changes in a novel Alzheimer’s disease mouse model. Manuscript in preparation.

Acknowledgements

The BRAINSPACE project received support from the EBRAINS infrastructure with funding from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Framework Partnership Agreement No. 650003 (HBP FPA).

Contact us

For questions relating to the BRAINSPACE article, contact the lead author. For advice on using the tools in the QUINT workflow, contact [email protected]