This web page contains the most recent versions of the imaging data supporting the article: ## A three-dimensional stereotaxic atlas of the gray short-tailed opossum (*Monodelphis domestic*a) brain ## Piotr Majka, Natalia Chlodzinska, Krzysztof Turlejski, Tomasz Banasik, Ruzanna L. Djavadian, Władysław P. Węglarz, Daniel K. Wójcik ### ABSTRACT ### The gray short-tailed opossum (*Monodelphis domestica*) is a small marsupial gaining recognition as a laboratory animal in biomedical research. Despite numerous studies on opossum neuroanatomy, a consistent and comprehensive neuroanatomical reference for this species is still missing. Here we present the first three-dimensional, multimodal atlas of the *Monodelphis* opossum brain. It is based on four complementary imaging modalities: high resolution ex-vivo magnetic resonance images, micro-computed tomography scans of the cranium, images of the face of the cutting block, and series of sections stained with the Nissl method and for myelinated fibers. Individual imaging modalities were reconstructed into a three-dimensional form and then registered to the MR image by means of affine and deformable registration routines. Based on a superimposition of the 3D images, 113 anatomical structures were demarcated and the volumes of individual regions were measured. The stereotaxic coordinate system was defined using a set of cranial landmarks: interaural line, bregma, and lambda, which allows for easy expression of any location within the brain with respect to the skull. The atlas is released under the Creative Commons license and available through various digital atlasing web services. ## Available imaging data ## The data below is distributed under the terms of the [Creative Commons Attribution 4.0 International License][1]. ### Three-dimensional images localized in the stereotaxic reference system ### All images are provided as [Niftii][2] files, represented at 50 μm isotropic resolution. File size provided for files larger than 50 MB. 1. Reference MR image ([download][3], **75 MB**), 2. MR image captured 48 hours after perfusion ([download][4], **75 MB**), 2. Segmentation into individual brain structures ([download][5]), and a description of the parcellation ([download][6]), 3. Blockface image stack affinely coregistered to the reference MR image ([download][7]), 4. 3D reconstruction of the brain image based on the Nissl-stained serial sections affinely coregistered to the MR image ([download][8]), 5. 3D reconstruction of the brain image based on the Nissl-stained serial sections coregistered to the MR image ([download][9]), 6. 3D reconstruction of the brain image based on the myelin-stained serial sections affinely coregistered to the MR image ([download][10]), 7. 3D reconstruction of the brain image based on the myelin-stained serial sections coregistered to the MR image ([download][11]), 8. Micro-computed tomography scan of the skull ([download][12]). ### Unprocessed imaging data used to produce the atlas ### 1. Unprocessed MR images in Nifti format ([download][13], **300 MB**), 2. Micro-computed tomography scan of the skull in Nifti format ([download][14], **1.5 GB**), 3. Blockface images in cr2 format ([download][15], **6 GB**), 4. Images of myelin-stained sections in tiff format ([download][16], **8 GB**), 5. Images of Nissl-stained sections in tiff format ([download][17], **8 GB**). ### Other 3D images ### 1. Nissl-stained brain volume affinely registered to MRI ([download][18]), 2. Nissl-stained brain volume deformably registered to MRI ([download][19]), 3. Nissl to MRI deformation field ([download][20], **200 MB**), 4. MRI to Nissl deformation field ([download][21], **190 MB**), 5. Myelin-stained brain volume affinely coregistered to MRI ([download][22]), 6. Myelin-stained brain volume deformably coregistered to MRI ([download][23]), 7. Myelin to MRI deformation field ([download][24], **265 MB**), 8. MRI to myelin deformation field ([download][25], **250 MB**). ### Additional online resources ### 1. [Segmentation][26] available via the 3d Brain Atlas Reconstructor Service, 2. [Atlas available via the Scalable Brain Atlas][27], a web-based display engine for brain atlases, 3. [Various visualizations of the atlas][28], a YouTube movie, 4. [ItkSnap][29], a software for viewing and segmenting three-dimensional images. [1]: https://creativecommons.org/licenses/by/4.0/ [2]: https://nifti.nimh.nih.gov/ [3]: https://osf.io/ydwqs/download?version=1 [4]: https://osf.io/38q7a/download?version=1 [5]: https://osf.io/p3nqv/download?version=1 [6]: https://osf.io/6rgk8/download [7]: https://osf.io/qz8sh/download [8]: https://osf.io/nd273/download [9]: https://osf.io/jp6dn/download [10]: https://osf.io/nd273/download [11]: https://osf.io/h8pnc/download [12]: https://osf.io/2nw3b/download [13]: https://files.osf.io/v1/resources/hbx5p/providers/osfstorage/59a53e789ad5a10253d6b207/?zip= [14]: https://files.osf.io/v1/resources/hbx5p/providers/osfstorage/59a53eda6c613b0259256cd4/?zip= [15]: https://files.osf.io/v1/resources/hbx5p/providers/osfstorage/59a51b8fb83f69025d20ee1c/?zip= [16]: https://files.osf.io/v1/resources/hbx5p/providers/osfstorage/59a53e9a9ad5a10255d6c9f2/?zip= [17]: https://files.osf.io/v1/resources/hbx5p/providers/osfstorage/59a53e8e9ad5a10253d6b20d/?zip= [18]: https://osf.io/nwzjc/download [19]: https://osf.io/qv7wk/download [20]: https://osf.io/xq3ct/download [21]: https://osf.io/em9rx/download [22]: https://osf.io/w5drt/download [23]: https://osf.io/h8pnc/download [24]: https://osf.io/6zk87/download [25]: https://osf.io/we4yz/download [26]: http://www.3dbar.org:8080/getCafInfoPage?cafDatasetName=pos_0.1 [27]: http://scalablebrainatlas.incf.org/main/coronal3d.php?template=OPSM14& [28]: https://youtu.be/kbXB3Y4DJrk [29]: http://www.itksnap.org/