Published: 17 August 2022| Version 1 | DOI: 10.17632/2svx788ddf.1
Yongsoo Kim


This package is the version 001 release of the Kim Lab Developmental CCF (KimLabDevCCFv001). KimLabDevCCF is a 3D whole mouse brain multimodal common coordinate framework. v001 includes multimodal templates (STPT, LSFM, and MRI) for the adult mouse brain (P56) as well as continuous 3D annotations segmented according to Luis Puelles' Developmental Vertebrate Ontology. The package contains the following files representative of the P56 mouse brain at 10um, 25um, and 50um isotropic resolution: - The CCFv3 Template: CCFv3_average_template_ASL_Oriented_u16_10um.nii.gz - Developmental Atlas segmentations based on the Developing Mouse Brain Atlas: KimLabDevCCFv001_Annotations_ASL_Oriented_10um.nii.gz - LSFM average template registered to the Allen CCFv3 Space: KimLabDevCCFv001_iDiscoLSFM2CCF_avgTemplate_ASL_Oriented_10um.nii.gz - The Allen Developing Mouse Brain Atlas Ontology Structure modified to include labels present in the KimLabDevCCFv001 that are not present in the Allen ontology: KimLabDevCCFv001_MouseOntologyStructure.csv (additional labels - MRI average templates of 6 contrasts (a0, adc, dwo, fa, MTR, T2) registered to the Allen CCFv3 Space: KimLabDevCCFv001_P56_MRI-a02CCF_avgTemplate_ASL_Oriented_10um.nii.gz KimLabDevCCFv001_P56_MRI-adc2CCF_avgTemplate_ASL_Oriented_10um.nii.gz KimLabDevCCFv001_P56_MRI-dwi2CCF_avgTemplate_ASL_Oriented_10um.nii.gz KimLabDevCCFv001_P56_MRI-fa2CCF_avgTemplate_ASL_Oriented_10um.nii.gz KimLabDevCCFv001_P56_MRI-MTR2CCF_avgTemplate_ASL_Oriented_10um.nii.gz KimLabDevCCFv001_P56_MRI-T22CCF_avgTemplate_ASL_Oriented_10um.nii.gz *Note: All data in this release version are registered to the Allen Institute CCFv3 morphological space.



Pennsylvania State University


Neuroinformatics, Brain Imaging, Atlas