Attention: The Keycloak upgrade has been completed. As this was a major upgrade, there may be some unexpected issues occurring. Please report any issues you find to support by using the contact form found at https://www.ebrains.eu/contact/. Thank you for your patience and understanding. 


Changes for page Atlas pipeline workflow

Last modified by drodarie on 2023/11/13 12:31
From version 17.2
edited by drodarie
on 2023/03/26 17:04
Change comment: There is no comment for this version
To version 15.1
edited by drodarie
on 2023/03/26 16:58
Change comment: Deleted image "workflow_complete_plot.png"

Summary

Details

Page properties
Content
... ... @@ -17,18 +17,18 @@
17 17  (((
18 18  = Content =
19 19  
20 -This collab is meant for modelists interested in using [[Blue Brain atlas suite>>https://github.com/BlueBrain/atlas-suite]] [1] and the [[Brain Scaffold Builder>>https://github.com/dbbs-lab/bsb]] (BSB) [2] to build circuits of the mouse brain.
20 +This collab is meant for modelists interested in using Blue Brain atlas [1] tools and the Brain Scaffold Builder (BSB) [2] to build circuits of the mouse brain.
21 21  
22 22  This collab contains notebooks to present the mouse brain cell atlas pipeline: its steps and results.
23 23  
24 24  Through these notebooks, you should learn:
25 25  
26 -* How to manipulate the Allen Brain reference atlases and brain region hierarchy, using the [[voxcell>>https://github.com/BlueBrain/voxcell]] library.
27 -* (% style="color:#999999" %)How to realign ISH datasets to the Nissl reference atlas (introduction to [[Deep-Atlas>>https://github.com/BlueBrain/Deep-Atlas]] [3]).
28 -* How to compute the orientation field followed by the neurons inside a region (introduction to [[atlas-direction-vectors>>https://github.com/BlueBrain/atlas-direction-vectors]]).
26 +* How to manipulate the Allen Brain reference atlases and brain region hierarchy, using the voxcell library.
27 +* (% style="color:#999999" %)How to realign ISH datasets to the Nissl reference atlas (introduction to Deep-Atlas [3]).
28 +* How to compute the orientation field followed by the neurons inside a region (introduction to atlas-direction-vectors).
29 29  * (% style="color:#999999" %)How to compute the depth field following the orientation field.
30 -* How to compute cell, neuron and glia densities in each region of the mouse brain (first introduction to [[atlas-densities>>https://github.com/BlueBrain/atlas-densities]]).
31 -* (% style="color:#999999" %)How to estimate neuron sub-type densities based on literature findings (second introduction to (%%)[[atlas-densities>>https://github.com/BlueBrain/atlas-densities]](% style="color:#999999" %)).
30 +* How to compute cell, neuron and glia densities in each region of the mouse brain (introduction to atlas-densities).
31 +* (% style="color:#999999" %)How to estimate neuron sub-type densities based on literature findings.
32 32  * (% style="color:#999999" %)How to refine neuron densities based on linear densities.
33 33  * (% style="color:#999999" %)How to scale, rotate and bend neuron morphologies, based on the orientation and depth fields.
34 34  * (% style="color:#999999" %)How to construct a circuit based on the resulting cell atlas model in BSB.
workflow_complete_plot.tif
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.drodarie
Size
... ... @@ -1,0 +1,1 @@
1 +4.6 MB
Content
workflow_plot.tif
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.drodarie
Size
... ... @@ -1,0 +1,1 @@
1 +2.4 MB
Content