= Supplementary material =

Web page http://www.3dbar.org/wiki/barPossumSupplement contains the most recent versions of the supplementary materials for the article:

== A three-dimensional stereotaxic atlas of the gray short-tailed opossum (''Monodelphis domestica'') 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 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. 

== The following supplementary materials are available: ==


=== Volumes localized in the stereotaxtic reference system ===

(all volumes are represented at 50μm isotropic resolution)

1. Reference MR brain volume ([http://doc.3dbar.org/possum/01/mri_reference_in_srs.nii.gz Download], 14MB),
1. Segmentation of the MR brain volume ([http://doc.3dbar.org/possum/01/segmentation_in_srs.nii.gz Download], 0.8MB; [http://doc.3dbar.org/possum/01/labels.txt labels description]),
3. Blockface volume - affinely coregistered with the reference MR ([http://doc.3dbar.org/possum/01/blockface_volume_affine_in_srs.nii.gz Download], 16.4MB),
4. Nissl-stained brain volume:
   a. affinely coregistered ([http://doc.3dbar.org/possum/01/nissl_stain_volume_affine_in_srs.nii.gz Download], 17.1MB),
   b. deformably coregistered with MRI ([http://doc.3dbar.org/possum/01/nissl_stain_volume_deformed_in_srs.nii.gz Download], 16.8MB)
5. Myelin-stained brain volume:
   a. affinely coregistered with MRI ([http://doc.3dbar.org/possum/01/myelin_stain_volume_affine_in_srs.nii.gz Download], 20.7MB),
   b. deformably coregistered with MRI ([http://doc.3dbar.org/possum/01/myelin_stain_volume_deformed_in_srs.nii.gz Download], 21.7MB),
6. micro-CT skull image ([http://doc.3dbar.org/possum/01/micro_ct_in_srs.nii.gz Download], 20.6MB),


=== Additional online resources ===

1. [http://www.3dbar.org:8080/getCafInfoPage?cafDatasetName=pos_0.1 Segmentation] available via the [http://www.3dbar.org:8080/ 3d Brain Atlas Reconstructor Service]. 
2. [http://scalablebrainatlas.incf.org/main/coronal3d.php?template=OPSM14& Atlas available via the Scalable Brain Atlas] web-based display engine for brain atlases
3. [https://youtu.be/kbXB3Y4DJrk Vatious visualzations of the atlas] on Youtube
4. [http://www.itksnap.org/ ItkSnap Website] Software for viewing and segmenting three dimensional images.


=== Other 3D images ===

(not localized in stereoraxic reference frame)

1. Nissl-stained brain volume affinely registered to MRI ([http://doc.3dbar.org/possum/02/nissl_stain_affine.nii.gz rgb volume], 18.3MB),
2. Nissl-stained brain volume nonlineary registered to MRI ([http://doc.3dbar.org/possum/02/nissl_stain_deformed.nii.gz rgb volume], 18.1MB),
3. Nissl to MRI deformation field ([http://doc.3dbar.org/possum/02/nissl_to_mri_warp.nii.gz Download], 202MB),
4. MRI to Nissl deformation field ([http://doc.3dbar.org/possum/02/mri_to_nissl_warp.nii.gz Download], 190MB),

5. Myelin-stained brain volume affinely coregistered to MRI ([http://doc.3dbar.org/possum/02/myelin_stain_affine.nii.gz rgb volume], 22.2MB),
6. Myelin-stained brain volume nonlineary coregistered to MRI ([http://doc.3dbar.org/possum/02/nissl_stain_deformed.nii.gz rgb volume], 23.2MB),
7. Myelin to MRI deformation field ([http://doc.3dbar.org/possum/02/myelin_to_mri_warp.nii.gz Download], 264MB),
8. MRI to myelin deformation field ([http://doc.3dbar.org/possum/02/mri_to_myelin_warp.nii.gz Download], 248MB).