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mleiwe / PathologyRegistrationPipeline

A Project for the Merbl lab at Cornell. The aim is to create a registration pipeline whereby large .bif files of histological sections can be put in registration with an MRI template in order to view the anatomy in high resolution.
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Identify a dog brain MRI template as a test #11

Open mleiwe opened 7 months ago

mleiwe commented 7 months ago

Task do some searching to identify an initial atlas to begin with, before wasting time and money performing our own MRI

mleiwe commented 7 months ago

I found three possibilities

  1. University of Minnesota has a Dog Brain atlas but it is annotated so not ideal --> Tom Fletcher
  2. R Datta, et al. 2012 A Digital Atlas of the Dog Brain, old and the dataset is not downloadable anymore https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3527386/
  3. Johnson et al. 2019 Stereotactic Cortical Atlas of the Domestic Canine Brain --> Erica Barry's lab at Cornel I was able to download an atlas to work with here. So I will go with this one. https://www.nature.com/articles/s41598-020-61665-0#data-availability This is a 0.5 x 0.5 x 0.5 mm voxel resolution so we may need a higher resolution, but for trial data it should work Image