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Welcome to the Brain/MINDS Marmoset Connectivity Resource. The official landing page for this resource is here : Brain/MIND data portal.
Here a link to the preprint of our manuscript:
Related work:
Video: Demonstration of the BMCR-Explorer.
The BMCR-Explorer is publicly available online. You might find our introduction helpful. Or directly start by clicking on one of the example images below. The BMCR-Explorer works best with google-chrome, 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 . We plan to release a downloadable offline version of the BMCR-Explorer in the future.
Figure: 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 BMCR-Explorer).
Figure: An anterograde and retrograde tracer (click on the figure to open the image in the BMCR-Explorer).
Figure: 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 BMCR-Explorer).
You can download the data from here. Further instructions for installing the Nora-stack app can be found here: Nora-Howto .
Our image data is published under the CC BY 4.0 license (https://creativecommons.org/licenses/by/4.0/deed.en).
The downloadable dataset also includes data derived from four atlases that are work of other groups, which you might find helpful in reproducing and exploring our findings. Please carefully read the accompanying ‘Readme’ files, as some of the data is released under different licenses. If you find these data useful and plan to use it, then you must cite the original work, and accept their licenses. A summary of the atlas licenses is provided below:
Video: Demonstration of the Nora-StackApp. The Nora-StackApp based on the nora medical imaging platform, which we extended with functions so that it interacts with BMCR-Explorer and flatmap stacks.
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 ATLAS, MARMOSET BRAIN MAPPING version 2 and 3, Brain/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.
Video: Demonstration of the warping field mapping from the STPT template image space to a human brain
Some code examples showing how to use the ANTs image registration toolkit to map marmoset brain images to a flatmap stack can be found here: https://github.com/BrainImageAnalysis/flatmap_stack/wiki.
Video: Demonstration of the warping field mapping from the STPT template image space to the 3D flatmap stack
We mapped all 145 retrograde tracer data from the MARMOSET BRAIN CONNECTIVITY ATLAS to our STPT template. The original data is publicly available under a http://creativecommons.org/licenses/by-sa/4.0/ license. We downloaded the cell data, mapped the data to our STPT template, generated cell density image stacks, and mapped them to flatmap-stacks as well. If you find these data useful and plan to use it, then you must cite the original work, and accept the MARMOSET BRAIN CONNECTIVITY ATLAS license (citing policy).
Video: The video above illustrates some of the major parts of our image processing pipeline. It is a bit outdated. By that time, we completed the image processing for 41 cortical injections.
Video: Anterograde tracer segmentation: Area 10 in the marmoset prefrontal cortex
Video: Anterograde tracer segmentation: Area 8a in the marmoset prefrontal cortex
Video: Anterograde tracer segmentation: Area 32 in the marmoset prefrontal cortex