Brain/MINDS Marmoset Connectivity Atlas


The BMCA is a new resource that provides access to anterograde and retrograde neuronal tracer data in the prefrontal cortex of a marmoset brain. It comprises post-processed data and tools for exploring and reviewing the data, and for integration with other marmoset brain image databases and cross-species comparisons. We visualize data of different individuals in a common reference space at an unprecedented high resolution. Major features are:

  • Image data of anterograde and retrograde neuronal tracers.
  • dMRI tracktography data that is associated with anterograde injection sites.
  • We integrated retrograde neural tracer data from the Marmoset Brain Connectivity Atlas project.
  • Transformation fields to between other marmoset brain image databases and atlas  (Brain/MINDS Marmoset Reference AtlasMarmoset Brain Mapping, Marmoset Brain Connectivity Atlas).
  • Transformation fields to the human MNI space
  • Flatmap stacks of neural tracer data and several brain atlases (Including the all neccesary data to map other image data to flatmap stacks).
  • The BMCA-Explorere and the Nora-StackApp for reviewing the data
  • A left-right symmetric population-average brain image template based on serial two-photon tomography along with a left-right symmetric population-average HARDI, Nissl, and backlight image.


More information can be found on our web-page ( and in our pre-print:

The Brain/MINDS Marmoset Connectivity Atlas: Exploring bidirectional tracing and tractography in the same stereotaxic space

H. Skibbe, M.F. Rachmadi, K. Nakae, C. E. Gutierrez, J. Hata, H. Tsukada, C. Poon, K. Doya, P. Majka, M. G. P. Rosa, H. Okano, T. Yamamori, S. Ishii, M. Reisert, A. Watakabe. In bioRxiv, Cold Spring Harbor Laboratory, 2022.


(username and password on page 23 in the pre-print)

The BMCA-Explorer (click here) is publicly available online. An overview about its functionality is shown in the video on the right. We prepared further videos that can help you to get started (click here). You can also directly try it out by clicking on one of the three example images below.

The BMCA-Explorer works best with google-chrome (and chromium browser), but should also work with the chromium, firefox and edge browsers. Safari might work. It also has touch support. It won’t work with the Microsoft Internet Explorer :-(.

BMCA-Explorer Example 1: An anterograde tracer segmentation mask on top of the original serial two-photon tomography image (click on the figure to open the image in the BMCA-Explorer).

BMCA-Explorer Example 3: A serial two-photon tomography image of an anterograde neural tracer in the marmoset brain (click on the figure to open the image in the BMCA-Explorer).

BMCA-Explorer Example 2: An anterograde and retrograde tracer (click on the figure to open the image in the BMCA-Explorer).

BMCA-Explorer Example 4: Two serial two-photon tomography images of anterograde neural tracers from two different marmoset brains (click on the figure to open the image in the BMCA-Explorer).

Mapping between the marmoset and the human brain

The BMCA provides a warping field between the STPT image space and the human MNI space. The video on the right shows an anterograde tracer segmentation that has been mapped from a marmoset brain to a human brain. The warping fields are publicly available (see Data-Download)


The Nora-StackApp is based on the nora medical imaging platform, which we extended with functions so that it interacts with BMCA-Explorer and flatmap stacks.

Flatmap-stacks mapping

A flatmap extents cortical flatmaps with cortical depth. It allows the exploration of tracer data in a coordinate system, where the plane defines the location on the marmoset cortex, and z the cortical depth. The mapping is publicly available:


You can download the data from here or here. The dataset includes the STPT template images (with a population average STPT background image, a population average Nissl image, a population average backlit image and a population average HARDI. It further incooperates measurements derived from the population average HARDI. It also includes the ANTs warping field that maps data from our STPT template space to a flatmap-stack, and ANTs warping fields to map between other marmoset brain atlases (MARMOSET BRAIN CONNECTIVITY ATLASMARMOSET BRAIN MAPPING version 2 and 3Brain/MINDS Marmoset Reference Atlas v1.1.0). It also includes the warping field between the STPT image space and the human MNI space, and a copy of the Nora-StackApp.

Related publications:

  • Connectional architecture of the prefrontal cortex in the marmoset brain. Watakabe., A, Skibbe, H., Nakae, K., Abe, H., Ichinohe, N., Wang, J., Takaji, M., Mizukami, H., Woodward, A., Gong, R., Hata, J., Okano, H., Ishii, S. & Yamamori., T. bioRxiv 2021.12.26.474213; doi:

Contact: The content of this page is maintained by the Brain Image Analysis Unit, Riken CBS. Please feel free to contact us with any questions or comments about the content. Contact information can be found on our homepage: