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Changes for page Atlas pipeline workflow

Last modified by drodarie on 2023/11/13 12:31
From version 17.1
edited by drodarie
on 2023/03/26 16:58
Change comment: Deleted image "workflow_plot.tif"
To version 20.1
edited by drodarie
on 2023/11/13 12:31
Change comment: There is no comment for this version

Summary

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Title
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1 -HBP Summit 2023 - Atlas pipeline workflow
1 +Atlas pipeline workflow
Content
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17 17  (((
18 18  = Content =
19 19  
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.
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.
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 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).
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]]).
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 (introduction to atlas-densities).
31 -* (% style="color:#999999" %)How to estimate neuron sub-type densities based on literature findings.
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" %)).
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 -* (% style="color:#999999" %)How to construct a circuit based on the resulting cell atlas model in BSB.
34 +* (% style="color:#999999" %)How to construct a circuit based on the resulting cell atlas model in [[BSB>>https://github.com/dbbs-lab/bsb]].
35 35  
36 36  Each item in the list correspond to a notebook in the lab. Items in grey are notebooks still in preparation and will be integrated in the HBP collab, as soon as possible.
37 37  
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42 42  
43 43  Some parts of the notebooks might require more than the 2GB RAM memory available on the HBP lab. These steps will be highlighted in the notebook.
44 44  
45 +
45 45  = About the figure. =
46 46  
47 47  **Figure 1. Mouse declive cell placement workflow:**