Whole Mouse Head and Brain Imaging Data

Comprehensive collection of standardized datasets for the Brain Architecture Project.

Available Data Sets

• Coronal Whole Head Download ZIP
• Sagittal Whole Head Download ZIP
• Transverse Whole Head Download ZIP
• Coronal Brain Download ZIP
• Sagittal Brain Download ZIP
• Transverse Brain Download ZIP

Available Data

Each .zip contains the following data:

Histology

• Nissl stain (p56+-7, .46 in-plane resolution, 10um between planes)
  • lossless .jp2
  • lossy .jp2
  • downsampled .tif
  • downsampled .png
  • metadata .txt
• Myelin stain (p56+-7, .46 in-plane resolution, 10um between planes)
  • lossless .jp2
  • lossy .jp2
  • downsampled .tif
  • downsampled .png
  • metadata .txt

Radiology

• Primary Modality (in vivo)
  • T2w in vivo (0.1mm in-plane, 0.5mm thru-plane)
    • Filename (original): t2w.nii.gz (in data/invivo/ folder)
    • Filename (proc): t2w_rpg_n4.nii.gz (in t2w_proc/invivo/ folder)
• Secondary Modalities (in vivo)
  • Diffusion (multishell; 0.1mm in-plane, 0.5mm thru-plane)
    • Filename (original): dwi.nii.gz (in data/invivo/ folder)
    • Filename (proc): dwi_denoised_rpg_eddy.nii.gz (in dwi_proc/invivo/ folder)
• Derived Modalities (in vivo) [In same space as Diffusion modality above]
  • Diffusion tensor (4D vol, 6 param/voxel: Dxx, Dyy, Dzz, Dxy, Dxz, Dyz)
    • Filename: dki_tensor.nii.gz (in dwi_maps_head/invivo/../../udki/ folder)
  • Principal diffusion direction(4D vol, 3 param/voxel: Dx, Dy, Dz)
    • Filename: dki_pdd.nii.gz (in dwi_maps_head/invivo/../../udki/ folder)
  • Fractional Anisotropy
    • Filename: dki_fa.nii.gz (in dwi_maps_head/invivo/../../udki/ folder)
  • Axial diffusivity
    • Filename: dki_ad.nii.gz (in dwi_maps_head/invivo/../../udki/ folder)
  • Radial diffusivity
    • Filename: dki_rd.nii.gz (in dwi_maps_head/invivo/../../udki/ folder)
  • Mean diffusivity
    • Filename: dki_md.nii.gz (in dwi_maps_head/invivo/../../udki/ folder)
  • Axial kurtosis
    • Filename: dki_ak.nii.gz (in dwi_maps_head/invivo/../../udki/ folder)
  • Radial kurtosis
    • Filename: dki_rk.nii.gz (in dwi_maps_head/invivo/../../udki/ folder)
  • Mean kurtosis
    • Filename: dki_mk.nii.gz (in dwi_maps_head/invivo/../../udki/ folder)
  • Signal 0th order rotational invariants (4D vol, 4 param/voxel: S0 per shell)
    • Filename: smi_S0.nii.gz (in dwi_maps_head/invivo/../../smi/ folder)
  • Signal 2th order rotational invariants (4D vol, 4 param/voxel: S2 per shell)
    • Filename: smi_S2.nii.gz (in dwi_maps_head/invivo/../../smi/ folder)
  • Signal 4th order rotational invariants (4D vol, 4 param/voxel: S4 per shell)
    • Filename: smi_S4.nii.gz (in dwi_maps_head/invivo/../../smi/ folder)
  • Standard Model: Intra-axonal water fraction
    • Filename: smi_f.nii.gz (in dwi_maps_head/invivo/../../smi/ folder)
  • Standard Model: Intra-axonal diffusivity
    • Filename: smi_D_a.nii.gz (in dwi_maps_head/invivo/../../smi/ folder)
  • Standard Model: Extra-axonal axial diffusivity
    • Filename: smi_D_e_par.nii.gz (in dwi_maps_head/invivo/../../smi/ folder)
  • Standard Model: Extra-axonal radial diffusivity
    • Filename: smi_D_e_perp.nii.gz (in dwi_maps_head/invivo/../../smi/ folder)
  • Standard Model: Free water fraction
    • Filename: smi_ffw.nii.gz (in dwi_maps_head/invivo/../../smi/ folder)
  • Standard Model: FOD second order rotational invariant
    • Filename: smi_p2.nii.gz (in dwi_maps_head/invivo/../../smi/ folder)
  • Standard Model: FOD fourth order rotational invariant
    • Filename: smi_p4.nii.gz (in dwi_maps_head/invivo/../../smi/ folder)
• Primary Modality (ex vivo)
  • T2w ex vivo (0.1mm in-plane, 0.5mm thru-plane)
    • Filename (original): t2w.nii.gz (in data/exvivo/ folder)
    • Filename (proc): t2w_rpg_n4.nii.gz (in t2w_proc/exvivo/ folder)
• Secondary Modalities (ex vivo)
  • Diffusion (multishell; 0.1mm in-plane, 0.5mm thru-plane)
    • Filename (original): dwi.nii.gz (in data/exvivo/ folder)
    • Filename (proc): dwi_denoised_rpg_eddy.nii.gz (in dwi_proc/exvivo/ folder)
• Derived Modalities (ex vivo) [In same space as Diffusion modality above]
  • Diffusion tensor (4D vol, 6 param/voxel: Dxx, Dyy, Dzz, Dxy, Dxz, Dyz)
    • Filename: dki_tensor.nii.gz (in dwi_maps_head/exvivo/../../udki/ folder)
  • Principal diffusion direction(4D vol, 3 param/voxel: Dx, Dy, Dz)
    • Filename: dki_pdd.nii.gz (in dwi_maps_head/exvivo/../../udki/ folder)
  • Fractional Anisotropy
    • Filename: dki_fa.nii.gz (in dwi_maps_head/exvivo/../../udki/ folder) -Axial diffusivity
    • Filename: dki_ad.nii.gz (in dwi_maps_head/exvivo/../../udki/ folder)
  • Radial diffusivity
    • Filename: dki_rd.nii.gz (in dwi_maps_head/exvivo/../../udki/ folder)
  • Mean diffusivity
    • Filename: dki_md.nii.gz (in dwi_maps_head/exvivo/../../udki/ folder)
  • Axial kurtosis
    • Filename: dki_ak.nii.gz (in dwi_maps_head/exvivo/../../udki/ folder)
  • Radial kurtosis
    • Filename: dki_rk.nii.gz (in dwi_maps_head/exvivo/../../udki/ folder)
  • Mean kurtosis
    • Filename: dki_mk.nii.gz (in dwi_maps_head/exvivo/../../udki/ folder)
  • Signal 0th order rotational invariants (4D vol, 4 param/voxel: S0 per shell)
    • Filename: smi_S0.nii.gz (in dwi_maps_head/exvivo/../../smi/ folder)
  • Signal 2th order rotational invariants (4D vol, 4 param/voxel: S2 per shell)
    • Filename: smi_S2.nii.gz (in dwi_maps_head/exvivo/../../smi/ folder)
  • Signal 4th order rotational invariants (4D vol, 4 param/voxel: S4 per shell)
    • Filename: smi_S4.nii.gz (in dwi_maps_head/exvivo/../../smi/ folder)
  • Standard Model: Intra-axonal water fraction
    • Filename: smi_f.nii.gz (in dwi_maps_head/exvivo/../../smi/ folder)
  • Standard Model: Intra-axonal diffusivity
    • Filename: smi_D_a.nii.gz (in dwi_maps_head/exvivo/../../smi/ folder)
  • Standard Model: Extra-axonal axial diffusivity
    • Filename: smi_D_e_par.nii.gz (in dwi_maps_head/exvivo/../../smi/ folder)
  • Standard Model: Extra-axonal radial diffusivity
    • Filename: smi_D_e_perp.nii.gz (in dwi_maps_head/exvivo/../../smi/ folder)
  • Standard Model: Still water fraction (DOT)
    • Filename: smi_ffw.nii.gz (in dwi_maps_head/exvivo/../../smi/ folder)
  • Standard Model: FOD second order rotational invariant
    • Filename: smi_p2.nii.gz (in dwi_maps_head/exvivo/../../smi/ folder)
  • Standard Model: FOD fourth order rotational invariant
    • Filename: smi_p4.nii.gz (in dwi_maps_head/exvivo/../../smi/ folder)
• CT (50um resolution)

Analytic Results

• Averaged T2w in vivo volume as reference space
• 20um^3 isotrpic co-registered Nissl Volume
• 20um^3 isotrpic co-registered Myelin Volume
• 20um^3 isotropic T2w in-vivo MRI, resampled
• 20um^3 isotropic T2w ex-vivo MRI, resampled
• Slice MR & CT volumes mapped to reference space
  • virtual sections matched with alternate N/MY histology
• Superimposed atlas region boundaries

Access

All datasets are available under GNU GPL v3 license.