= Supplementary material =

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

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==  ==


= ABSTRACT =

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== The following supplementary materials are available: ==


=== Summary of the parameters used during the reformable reconstruction ===

1. [attachment:oossum_brain_atlas_article_deformable_reconstruction_parameters.pdf See attached pdf file]


=== 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).