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B3.1 #184

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B3.1 #184

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a2f74dc
Removing some addons that are not needed anymore.
marwan-abdellah Feb 20, 2023
c364ea7
Minor bug fixes.
marwan-abdellah Feb 20, 2023
a56311c
Adding a simple utility to visualize color-coded synapses.
marwan-abdellah Feb 20, 2023
e51a059
Addign the custom synaptic visualization.
marwan-abdellah Feb 21, 2023
4974ff3
Visualizing excitatory and inhibitory synapses.
marwan-abdellah Feb 21, 2023
97d02ec
Using dicts instead of lists.
marwan-abdellah Feb 21, 2023
4d9e0ec
Adding new functions for synapse visualization.
marwan-abdellah Feb 22, 2023
2c20303
Using particle system to visualize large amounts of synapses.
marwan-abdellah Feb 23, 2023
8f3c859
Minor improvements in the particle system.
marwan-abdellah Feb 27, 2023
1e1aaed
Renaming the synapses add-ons untill further notice.
marwan-abdellah Feb 27, 2023
a1b84ac
Minor clean ups.
marwan-abdellah Feb 27, 2023
9dae99b
Displaying the excitatory and inhibitory synapses.
marwan-abdellah Feb 27, 2023
21f699f
Refactoring the synaptics.
marwan-abdellah Feb 27, 2023
f34adfd
Minor fixes.
marwan-abdellah Feb 27, 2023
6d51fd1
Adding option to make unifying radius for all the branches.
marwan-abdellah Feb 27, 2023
9e601e3
Minor.
marwan-abdellah Feb 27, 2023
c67de3b
Visualizing synapses based on pre- and post-synaptic mtypes.
marwan-abdellah Feb 27, 2023
dd53389
Adding the visualization of the etypes as well.
marwan-abdellah Feb 27, 2023
539e841
Adding support to change the colors of the individual arbors of the s…
marwan-abdellah Feb 28, 2023
9eeda22
Adding the synaptic pathways usecase.
marwan-abdellah Feb 28, 2023
e7870f5
Adjusting the spines orientation.
marwan-abdellah Mar 1, 2023
8af33a8
Synaptic pathways.
marwan-abdellah Mar 1, 2023
35cf703
Starting to add the synaptics interface.
marwan-abdellah Mar 1, 2023
feb3fb4
Adjusting the synapses loading UI and preparing to the implementation.
marwan-abdellah Mar 2, 2023
a7bca64
Improving circuit loading and completing the synapse visualization op…
marwan-abdellah Mar 6, 2023
a8b6aa1
Further cleanups for the I/O panel.
marwan-abdellah Mar 6, 2023
13da721
Minor.
marwan-abdellah Mar 6, 2023
76a7cb0
Improving the loading mechanism.
haitham-shaban Mar 6, 2023
32c808c
Cleaning the loading.
marwan-abdellah Mar 7, 2023
3bcebf7
Color coding by types.
marwan-abdellah Mar 7, 2023
b07bf86
Minor.
marwan-abdellah Mar 8, 2023
82d84cb
Further use cases and cleanups.
marwan-abdellah Mar 8, 2023
21e8480
Adding neuron to the scene with the synapses.
marwan-abdellah Mar 8, 2023
d09fa2d
Cleaning the UI.
marwan-abdellah Mar 8, 2023
b3ff7d6
Minor tweaks.
marwan-abdellah Mar 8, 2023
8999201
Minor cleanups.
marwan-abdellah Mar 8, 2023
7436611
Updating the copyrights.
marwan-abdellah Mar 8, 2023
9c9e60a
Addressing the centering issue.
haitham-shaban Mar 12, 2023
fce4660
Fixing the synaptic pathways.
marwan-abdellah Mar 13, 2023
e5927ca
Adding the synaptic pair options and synapses counts.
marwan-abdellah Mar 14, 2023
85745d2
Synaptics drawing.
marwan-abdellah Mar 14, 2023
bd84de4
Refactoring the interface.
marwan-abdellah Mar 15, 2023
c9be895
Refactoring the morphology panel.
marwan-abdellah Mar 15, 2023
4a89945
Minor.
haitham-shaban Mar 15, 2023
f15f372
Cleaning the morphology panel.
marwan-abdellah Mar 16, 2023
1999ca2
Cleanups.
marwan-abdellah Mar 16, 2023
6ad02c8
More improvements.
marwan-abdellah Mar 16, 2023
f1e21a6
Collections.
marwan-abdellah Mar 16, 2023
2ea5d18
Minor.
marwan-abdellah Mar 16, 2023
ef80b95
Minor.
haitham-shaban Mar 19, 2023
ffb970a
Resolving the dendrogram issue.
marwan-abdellah Mar 20, 2023
b479c37
Adjusting the morphology reconstruction options.
marwan-abdellah Mar 20, 2023
3031bf9
Cleaning the meshing panel.
marwan-abdellah Mar 20, 2023
f2cd874
Meshing.
marwan-abdellah Mar 20, 2023
2d664fc
About page.
marwan-abdellah Mar 21, 2023
d580d8e
Updating OS.
marwan-abdellah Mar 21, 2023
61b2aca
Analysis results.
marwan-abdellah Mar 21, 2023
1941785
Analysis.
marwan-abdellah Mar 21, 2023
187951f
Refactoring the soma panel.
marwan-abdellah Mar 21, 2023
2373929
Soma reconstruction.
marwan-abdellah Mar 21, 2023
1c81345
Minor updates.
marwan-abdellah Mar 22, 2023
3cf567a
Pathways.
marwan-abdellah Mar 24, 2023
c220eab
Minor.
marwan-abdellah Mar 24, 2023
c5db0d5
Synaptics.
marwan-abdellah Mar 24, 2023
981d07d
Synaptics. Target case.
marwan-abdellah Mar 27, 2023
bbc8386
Further cleanups, synaptics.
marwan-abdellah Mar 27, 2023
1ab6356
Rendering scale bar fix.
marwan-abdellah Mar 27, 2023
ddfc149
Target.
marwan-abdellah Mar 27, 2023
90fa95c
Projection.
marwan-abdellah Mar 27, 2023
6b343dd
Refactoring the edit panel.
marwan-abdellah Mar 28, 2023
6638a9c
Adding libsonata class.
marwan-abdellah Mar 28, 2023
64a2d33
Edits.
marwan-abdellah Mar 28, 2023
8ec2622
Minor.
marwan-abdellah Mar 28, 2023
beb1116
Adjusting the loading from circuits.
marwan-abdellah Mar 28, 2023
b2c2f6d
Documenting the BBP circuit.
marwan-abdellah Mar 28, 2023
98d839a
Cleaning the globals.
marwan-abdellah Mar 28, 2023
4017740
Synapse generation.
marwan-abdellah Mar 28, 2023
79e0c10
Fixing the soma center issue.
marwan-abdellah Mar 28, 2023
99f9fa8
Adding the voxelization builder.
marwan-abdellah Mar 29, 2023
4b91433
Use the soma from the meshing toolbox.
marwan-abdellah Mar 29, 2023
9116e22
Fixing the soma center issue.
marwan-abdellah Mar 29, 2023
4e73fb8
Adjusting the mesh generation panel.
marwan-abdellah Mar 29, 2023
68e26e0
Implemented the connected sections method in the Meshing builders.
marwan-abdellah Mar 29, 2023
6bc6ce9
Adding correct references.
marwan-abdellah Mar 29, 2023
424d489
Minor.
marwan-abdellah Mar 29, 2023
60c5b1e
Headers.
marwan-abdellah Mar 29, 2023
34d8374
Dates.
marwan-abdellah Mar 29, 2023
9cf9efa
Branching ops.
marwan-abdellah Mar 29, 2023
8c20491
Refactoring and cleaning the meshing builders.
haitham-shaban Mar 30, 2023
b9d6786
Minor cleanups.
haitham-shaban Mar 30, 2023
c3f993b
Minor additions in the meshing and morphology interface.
haitham-shaban Mar 31, 2023
b5f71c2
Morphology toolbox.
haitham-shaban Apr 3, 2023
d7feb4e
Minor.
marwan-abdellah Apr 4, 2023
4788e4a
Cleaning the material generation and storage.
marwan-abdellah Apr 12, 2023
a445dbc
Minor.
marwan-abdellah Apr 13, 2023
9e4e94b
Minor.
marwan-abdellah Apr 17, 2023
c65819a
Cleaning the morphology builder.
marwan-abdellah Apr 17, 2023
8b06044
Cleanups.
marwan-abdellah Apr 17, 2023
794397f
Adjusting the names of the materials.
marwan-abdellah Apr 17, 2023
8d1711b
Adjusting the color.
marwan-abdellah Apr 17, 2023
ebaf61d
Cleanups.
marwan-abdellah Apr 17, 2023
360530b
Minor.
marwan-abdellah Apr 17, 2023
524a8aa
Minor.
marwan-abdellah Apr 17, 2023
bd644d9
Adjusting the MetaBuilder.
marwan-abdellah Apr 17, 2023
055c911
Fixing some issues in the endfeet visualization and mesh geenrators.
marwan-abdellah Apr 18, 2023
c2d5dd4
Adjusting the morphology format.
marwan-abdellah Apr 24, 2023
7ecc3bc
Fixing a few bugs in the mesh builders and the Synaptics.
marwan-abdellah Apr 24, 2023
ffb925e
Meshes interface.
marwan-abdellah Apr 25, 2023
674795a
Minor.
marwan-abdellah Apr 25, 2023
efaa0e1
Union builder roughness.
marwan-abdellah Apr 25, 2023
55d5183
Adjusting the spine code.
marwan-abdellah Apr 25, 2023
1c22e99
Spine building.
marwan-abdellah Apr 25, 2023
527500a
Minor.
marwan-abdellah Apr 25, 2023
411d0d3
Minor adjustment to the union builder.
marwan-abdellah Apr 26, 2023
c59c837
Adjusting the circuit spines code.
marwan-abdellah Apr 27, 2023
2ab6ebb
Synapses and spines.
marwan-abdellah Apr 27, 2023
a3121b9
Adjusting the synaptics code.
marwan-abdellah Apr 27, 2023
0d7e32a
Some synaptics issue.
marwan-abdellah Apr 27, 2023
9ae1f7a
Synaptic pathways form script.
marwan-abdellah Apr 27, 2023
2552c23
Adding a new file to visualize groups of synaptic pathways.
marwan-abdellah May 8, 2023
bbf3697
Visualize multiple synapses.
marwan-abdellah May 8, 2023
3a146c4
Fixing the synaptics add-on.
marwan-abdellah May 10, 2023
417eae9
Merge branch 'master' into b3.1
marwan-abdellah May 10, 2023
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12 changes: 0 additions & 12 deletions data/spines-meshes/lq/spine_1.mtl

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1 change: 0 additions & 1 deletion data/spines-meshes/lq/spine_1.obj
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Expand Up @@ -380,7 +380,6 @@ vn 0.9821 -0.1666 0.0874
vn 0.3216 -0.9396 0.1172
vn 0.6748 0.2947 -0.6766
vn 0.9608 -0.2542 0.1104
usemtl color.basal_dendrites_skeleton_color_0_color
s 1
f 136//1 2//2 1//3
f 4//4 5//5 6//6
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12 changes: 0 additions & 12 deletions data/spines-meshes/lq/spine_2.mtl

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4 changes: 0 additions & 4 deletions data/spines-meshes/lq/spine_2.obj
Original file line number Diff line number Diff line change
@@ -1,6 +1,3 @@
# Blender v2.82 (sub 7) OBJ File: 'eyewire-neuron-em-stack.blend'
# www.blender.org
mtllib spine_2.mtl
o <bpy_struct,_Object("spine_2")>-simple_2.135
v 0.067481 -0.108317 2.775392
v 0.186313 -0.082456 2.723809
Expand Down Expand Up @@ -500,7 +497,6 @@ vn -0.1233 0.8594 0.4962
vn -0.9043 -0.3969 0.1570
vn 0.4998 -0.8020 0.3269
vn -0.4928 -0.3126 -0.8121
usemtl color.basal_dendrites_skeleton_color_0_color
s 1
f 2//1 49//2 1//3
f 15//4 7//5 12//6
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