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Reference brains for registration to Zebrafish Brain Browser

Burgess, Harold

Collection of larval zebrafish brain images that can be used to register confocal stacks to the Zebrafish Brain Browser.

Please see the Excel spreadsheet for descriptions of each file including the expression pattern within the brain. There are several options for registration using a pan-neuronal driver such as huC, and you may need to test several to determine which is the best match to the reference channel that you are using.

The vglut-ref-01.nii.gz is the original reference brain used to construct ZBB and will likely provide the most precise registrations. All other files were registered to ZBB using the vglut reference or other bridging registrations.

For information on the registration procedure, please see Marquart GD, Tabor KM, Horstick EJ, Brown M and Burgess HA (2017) High precision registration between zebrafish brain atlases using symmetric diffeomorphic normalization. GigaScience. 6:1-15.

Files (4.1 GB)
Name Size
bActin-gfp-ref-01.nii.gz
md5:08410ee79f4cc1b26ffaa53306c956a9
371.6 MB Download
File_Descriptions.xlsx
md5:2555df257b6a8275477aa81a087751cd
14.3 kB Download
gad1b-ref-01.nii.gz
md5:7f8be92cbee07b514c8e5844874e5758
255.0 MB Download
huc-campari-ref-01.nii.gz
md5:ac72a6bb5311ada957c710da513434e2
321.7 MB Download
huc-cer-ref-01.nii.gz
md5:2a1c045c4a45433162172951dcadfc99
245.6 MB Download
huc-gcamp5g-ref-01.nii.gz
md5:c39e52a58fcbf39822a8e36bb5c519d1
299.2 MB Download
huc-h2b-rfp-ref-01.nii.gz
md5:f81f10376cf175b2c0f08cd0e9ff5b61
104.3 MB Download
huc-lynTagRFPT-ref-01.nii.gz
md5:0079c26871de6be54288aca7d27987fc
309.3 MB Download
huc-mcar-ref-01.nii.gz
md5:e06b31a39a6c2a7631fee57bf5b348b7
316.0 MB Download
huc-nls-mcar-ref-01.nii.gz
md5:ef0aa0001018eb5c989c484288f198b3
359.6 MB Download
huc-syp-ref-01.nii.gz
md5:4de28cdc0e56e7bff0516cf576f5043a
308.4 MB Download
lyso-ref-01.nii.gz
md5:323600abd49fb5b3c6fb21badbd970dd
448.6 MB Download
terk-ref-01.nii.gz
md5:57b60eb369db0f878b4a3c8ef6f58e9d
323.4 MB Download
tuba-mcar-ref-01.nii.gz
md5:1b4da4b2f3cbf7b4c9d099f80ff5e8b0
253.6 MB Download
vglut-ref-01.nii.gz
md5:2dace2f53e2dc14f260938ea0092b47c
149.3 MB Download
  • Marquart GD, Tabor KM, Horstick EJ, Brown M and Burgess HA (2017) High precision registration between zebrafish brain atlases using symmetric diffeomorphic normalization. GigaScience. 6:1-15

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