Tools and Links

Useful Tools

Visualization, segmentation and manipulation of 3D data

• 3D slicer: https://www.slicer.org/

  We used this software for visualization, annotation (segmentation) and other purposes. Accepts NIfTI,
  nrrd, DICOM and other formats.

• itk-SNAP: http://www.itksnap.org/pmwiki/pmwiki.php

  We used this software for visualization and annotation (segmentation). Accepts NIfTI, nrrd, DICOM and
  other formats.

• FIJI: https://imagej.net/software/fiji/

  FIJI is an image processing package based on ImageJ2. It can be used to manipulate image data in various
  ways including transformation of NIfTI files into multipage TIFF files.

• FluoRender: https://www.sci.utah.edu/software/fluorender.html

  FluoRender is an interactive rendering tool for volumetric data. Accepts multipage TIFF files.

• Advanced Normalization Tools (ANTs): http://stnava.github.io/ANTs/

  ANTs can be used to transform our NIfTI data to other atlases. Transformation parameters are provided in
  the download page.

Marmoset Databases

• Marmoset Brain Connectivity Atlas: https://www.marmosetbrain.org/

  Retrograde tracer database for corticocortical connections.
  Referenced to “MBCA” atlas (0.04 x 0.04 x 0.5 [mm]).

• The Marmoset Brain Architecture: http://marmoset.brainarchitecture.org/

  Raw fluorescent tracer data for anterograde and retrograde tracers.
  Includes links to Marmoset Brain Connectivity Atlas.

• Marmoset Brain Mapping: https://marmosetbrainmapping.org/index.html

  High resolution MRI and dMRI data.
  V1.0 cortical atlas (0.15 mm isotropic).
  V2.0 pathway (0.08 mm isotropic).
  V3.0 population (0.2 mm isotropic).

• Digital Brain Atlas of the Common Marmoset (Callithrix jacchus): https://neuropathology.jp/marmoset_login/

  Various histological staining data for marmoset brain and spinal cord.

Brain/MINDS

• Details about the tracer injection activities in the first half of Brain/MINDS can be found here.