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Details about currently available atlases.

Atlas details

Introduction

The atlases are available in a standardised form, via the BrainGlobe Atlas API (or any software that uses it). However, each atlas varies slightly in the versions that are available (e.g. resolutions).

To use the atlases with the API directly, the unique key (e.g. example_mouse_100um must be used).

Atlases

Allen Mouse Brain Atlas at 10, 25, 50 and 100 micron resolutions

  • allen_mouse_10um
  • allen_mouse_25um
  • allen_mouse_50um
  • allen_mouse_100um

Allen Human Brain Atlas at 100 micron resolution

  • allen_human_500um

Max Planck Zebrafish Brain Atlas at 1 micron resolution

  • mpin_zfish_1um

Enhanced and Unified Mouse Brain Atlas at 10, 25, 50 and 100 micron resolutions

  • kim_mouse_10um
  • kim_mouse_25um
  • kim_mouse_50um
  • kim_mouse_100um

Smoothed version of the Kim et al. mouse reference atlas at 10, 25, 50 and 100 micron resolutions

  • osten_mouse_10um
  • osten_mouse_25um
  • osten_mouse_50um
  • osten_mouse_100um

Gubra's LSFM mouse brain atlas at 20 micron resolution

  • perens_lsfm_mouse_20um

3D version of the Allen mouse spinal cord atlas at 20 x 10 x 10 micron resolution

  • allen_cord_20um

AZBA: A 3D Adult Zebrafish Brain Atlas at 4 micron resolution

  • azba_zfish_4um

``Waxholm Space atlas of the Sprague Dawley rat brain at 39 micron resolution

  • whs_sd_rat_39um

3D Edge-Aware Refined Atlases Derived from the Allen Developing Mouse Brain Atlases (E13, E15, E18, P4, P14, P28 & P56)

  • admba_3d_e11_5_mouse_16um
  • admba_3d_e13_5_mouse_16um
  • admba_3d_e15_5_mouse_16um
  • admba_3d_e18_5_mouse_16um
  • admba_3d_p4_mouse_16.752um
  • admba_3d_p14_mouse_16.752um
  • admba_3d_p28_mouse_16.752um
  • admba_3d_p56_mouse_25um

Princeton Mouse Brain Atlas at 20 micron resolution

  • princeton_mouse_20um

Kim Lab Developmental CCF (P56) at 10 micron resolution with 8 reference images - STP, LSFM (iDISCO) and MRI (a0, adc, dwo, fa, MTR, T2)

  • kim_dev_mouse_stp_10um - "normal" CCF serial 2p template
  • kim_dev_mouse_idisco_10um - iDISCO LSFM template
  • kim_dev_mouse_mri_a0_10um - MRI a0 template
  • kim_dev_mouse_mri_adc_10um - MRI ADC (apparent diffusion coefficient) template
  • kim_dev_mouse_mri_dwi_10um - MRI DWI (diffusion-weighted imaging)template
  • kim_dev_mouse_mri_fa_10um - MRI FA (fractional anisotropy) template
  • kim_dev_mouse_mri_mtr_10um - MRI MTR (magnetic transfer ratio) template
  • kim_dev_mouse_mri_t2_10um - MRI T2 template