QuickNII - Serial section aligner to volumetric atlases
Key features:
- generate user defined cut planes through the atlas templates, matching the orientation of the cut plane of the 2D experimental image data, as a first step towards anchoring of images to the relevant atlas template
- propagate spatial transformations across series of sections following anchoring of selected images
Multi-modality atlasing datasets provided with QuickNII:
- Waxholm Space Atlas of the Sprague Dawley rat brain, version 2 and 3 (T2* MRI, DTI, and delineations at 39 μm resolution)
- Allen Mouse Brain Atlas reference atlas, CCFv3 (SST average template, grayscale Nissl volume reconstruction and delineations from 2015 and 2017 at 25 μm resolution)
Specifications
Recent Activity - Documents
QuickNII_user_manual_v1.5 posted by Maja Puchades on Feb 22
QuickNII user guide posted by Maja Puchades on Mar 27, 2019
Recent Activity - Forums
RE: Linux compatible version request posted by pmt on Jul 20, 2020
RE: Linux compatible version request posted by Gergely Csucs on Jul 14, 2020
RE: Linux compatible version request posted by Gergely Csucs on Jul 1, 2020
Linux compatible version request posted by pmt on Jun 30, 2020
RE: Free-form registration in QuickNII posted by Penelope Young on May 20, 2020
RE: Free-form registration in QuickNII posted by Gergely Csucs on May 20, 2020
RE: Free-form registration in QuickNII posted by Penelope Young on May 14, 2020
RE: Free-form registration in QuickNII posted by Gergely Csucs on May 14, 2020
Free-form registration in QuickNII posted by Penelope Young on May 14, 2020
RE: QSlicer posted by Harry Carey on Sep 24, 2019
Recent Activity - Files
QuickNII for Windows (x64): 2.2 release
QuickNII-Wine-patch.zip posted by Gergely Csucs on Jul 14, 2020
QuickNII for Windows (x64): 2.2 FileBuilder fix for Windows release
FileBuilder.zip posted by Gergely Csucs on Jul 10, 2020
QuickNII-WHSRat-v3.dmg posted by Gergely Csucs on Sep 20, 2019
QuickNII-ABAMouse-v3-2017.dmg posted by Gergely Csucs on Sep 20, 2019
QuickNII for Windows (x64): 2.2 release
QuickNII-WHSRat-v3.zip posted by Gergely Csucs on Sep 19, 2019
QuickNII for Windows (x64): 2.2 release
QuickNII-ABAMouse-v3-2017.zip posted by Gergely Csucs on Sep 19, 2019
QuickNII-WHSRat-v2.dmg posted by Gergely Csucs on May 28, 2019
QuickNII for Windows (x64): 2.2 release
QuickNII-WHSRat-v2.zip posted by Gergely Csucs on May 28, 2019
QuickNII-ABAMouse-v3-2015.dmg posted by Gergely Csucs on May 28, 2019
QuickNII for Windows (x64): 2.2 release
QuickNII-ABAMouse-v3-2015.zip posted by Gergely Csucs on May 28, 2019