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Atlas details

Details about currently available atlases.

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
  • whs_sd_rat_39um
  • 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
​
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Last modified 4mo ago