The Morphology Bounding Box Info field must be moved to the Morphology Analysis panel. The current location is not convenient and might be confusing.

In certain cases, the soma radius is set to zero. This raises an exception and causes an error sketching the morphologies.

Change Soma Base Color to Soma Color in the Soma Toolbox panel.

To make it further intuitive, it is recommended to add a little widget that can show the selected material prior to rendering the morphology or the mesh. This would it make it convenient to render the morphology or the mesh only once after seeing the materials following to their selections from the drop down menus.

If the end users selects the branching by Angles, for example in the Morphology Toolbox, when loading SWC files, the skeleton is not drawn and the following error is given:

line 242, in label_primary_and_secondary_sections_based_on_angles
    angle = parent_vector.angle(child_vector)
ValueError: Vector.angle(other): zero length vectors have no valid angle

To avoid confusion for external users or collaborators, hide the loading BBP circuit option if Brion is not installed on the system. Perform this step during an initialization step.

try:
    import brion
    BRION_COULD_BE_IMPORTED
catch:
    BRION_COULD_NOT_BE_IMPORTED

It would be easier for the users to see NeuroMorphoVis panel loaded once Blender is launched.

There is a redundant color filed in the Mesh Toolbox when the spines are ignore. This issue might confuse the users, therefore, it would be appreciated if the Spines Color option in the Mesh Toolbox is hidden when the spines are ignored.

To allow the users to manually add some fixes to the morphology skeleton, the skeleton must be sketched as a connected acyclic graph, where each node can be represented as a vertex and the the user can move or rotate this vertex. Using poly-lines cannot guarantee this implementation, so it is better to start from a single vertex at the origin and then extrude it along the skeleton.

The feature should be exposed to the user in the morphology analysis panel.

Soma Toolbox

Method: it's a bit unclear what are the complex and arbor methods, maybe a few words on what's under the hood or what's each method specificity would be useful

Base Color and Material: it seems that the color is taken in consideration only when the material is "Lambert Ward"

Subdivisions: of what? Also the default (5) seems to be the only one that gives satisfying results (lower: odd shapes, higher: too long to compute)

Simulation steps: Does not seem to affect the work, also the timeline at the bottom always goes up to 100

Quick Rendering Options: I've selected Resolution: 3600 and it was not quick. For a future version, a loading bar would be nice.

Meshes: export to OBJ is nice!

Morphology Toolbox

When reconstructed, some facets of the soma seem to be coplanar/overlapping with some facets of the dendrite and axons. Even though it makes sense in term of reconstruction, it might be better for visual purpose to truncate the axons/dendrite at the edge of the soma. EDIT: I later saw the option Arbor to Soma: All Disconnected but then we have gaps between soma and dendrites.

No option to save morphs in OBJ?

360 sequences are exported fine but only as a lit of png. Having an additional mp4 would be nice.

If we load morphologies with no apicals, the Analyse Morphology button does not show any results.

Some morphologies have zero radii. These samples cause issues and mesh reconstruction artifacts. It is therefore better to verify if the morphology has no samples with zero-radii before reconstructing it. It would be also nice to add in the analysis panel an item that should their number and distribution.

The current illumination used to render the morphologies or the meshes with the Lambert Ward shader looks dull. This must be fixed.

The scientists have requested a new feature in the analysis toolbox to allow them to compute the volumes and surface area of the following:

• Each segment in the morphology
• Each section in the morphology
• Total volume and surface area of each neurite in the morphology
• Total volume and surface area of the entire morphology
• Volume and surface area of the soma based on the sphere simplification or from the 3d mesh reconstructed from the soma toolbox.

The current rendering support of NeuroMorphoVis is limited to orthographic projection. In some cases, it would be nice to have an option to create perspective images for media generation.

It would be nice to add an option (for example, a simple checkbox) to draw scale bar on the images created from NeuroMorphoVis.

We can use NeuroMorphoVis to load SWC morphologies, visualize them and then we can use move the samples around to manually fix certain artifacts that we cannot be fixed automatically. Therefore, it would be nice to integrate an SWC exporter.

It is important for the analysis to add the soma information in a separate panel and then append the result to the morphology analysis results.

Using the Articulated Sections style to sketch the morphology in the Morphology Toolbox tab seems to have an issue. The morphology is not drawn and we get the following error:

Traceback (most recent call last):
  File "/home/abdellah/.config/blender/2.79/scripts/addons/NeuroMorphoVis/neuromorphovis/interface/ui/morphology_panel.py", line 417, in execute
    nmv.interface.ui_reconstructed_skeleton = builder.draw_morphology_skeleton()
  File "/home/abdellah/.config/blender/2.79/scripts/addons/NeuroMorphoVis/neuromorphovis/builders/skeleton/skeleton_builder.py", line 943, in draw_morphology_skeleton
    bevel_object=bevel_object))
  File "/home/abdellah/.config/blender/2.79/scripts/addons/NeuroMorphoVis/neuromorphovis/builders/skeleton/skeleton_builder.py", line 620, in draw_morphology_as_articulated_sections
    material_list=self.articulation_materials)
  File "/home/abdellah/.config/blender/2.79/scripts/addons/NeuroMorphoVis/neuromorphovis/builders/skeleton/skeleton_builder.py", line 255, in draw_section_terminals_as_spheres
    section_terminal_sphere = self.draw_section_terminal_as_sphere(root)
  File "/home/abdellah/.config/blender/2.79/scripts/addons/NeuroMorphoVis/neuromorphovis/builders/skeleton/skeleton_builder.py", line 212, in draw_section_terminal_as_sphere
    name='joint_%d' % section.id, color=self.options.morphology.articulation_color)
  File "/home/abdellah/.config/blender/2.79/scripts/addons/NeuroMorphoVis/neuromorphovis/geometry/object/sphere.py", line 81, in create_uv_sphere
    sphere_material = materials.create_default_material(name='sphere_color', color=color)
NameError: name 'materials' is not defined

location: <unknown location>:-1
location: <unknown location>:-1

Reconstructing a mesh with non-homogeneous colour apply only the soma colour for the whole morphology

Some users have requested to implement a meshing technique that can generate watertight meshes. Considering the complexity and the severe artefacts of the morphologies in general, mesh extrusion from simple geometry cannot be used. There are two solutions to implement this: either a volumetric-based (for example octree) reconstruction or a field-based method (like meta balls and meta objects).
Moreover, it would be appreciated if the artifacts of the morphologies are repaired before the reconstruction of the mesh and the soma profile was quite realistic.

The animation rendering support present in the Soma Toolbox, Morphology Toolbox and the Mesh Toolbox creates a sequence of frames. It would be nice if we can encode these frames into an .mp4 movie.

• This might require extra effort on Windows.

The piecewise watertight meshing algorithm might be limited for certain applications. It would be nice if we can integrate the implementation of Lasserre et al., 2011 in NeuroMorphoVis.

Implement the skeleton repair algorithm with bmeshes instead of meshes to make it faster to switch between the edited skeleton and the updated morphology. Similar to #50.

Remove the repeated morphology loading code in each panel and split it as a common utility.

Replace the export buttons with a drop down menu with all the options and a single button to export the mesh. This would make the UI less cluttered.

The current Developer Documentation is quite limited. It must be improved to get further collaborators and contributors.

For certain reasons, the subsurface scattering shader was removed from the shading drop down menu in the past. The shader is ready, but must be re-integrated again.

In the Soma Toolbox, the option Profile in the Methods section seems confusing according to the testers opinion. Change it to 2D Profile Points or only Profile Points.

The full arborization of the neurons is not right when I load a neuron with a specific GID from a circuit. This has been checked on BBP5. This must be fixed before the presentation.

We would like to add support to export the analysis results to analysis files for records.

This is a bug in the current version of NeuroMorphoVis. The Keep Camera and Lights in Scene checkbox in the Mesh Toolbox is always not checkable.

To improve the performance of the mesh reconstruction, implement the skinning algorithm with bmeshes instead of regular meshes. This might add an order of magnitude factor on the performance of the reconstruction function.

It would be nice to add support to load ASCII morphology (the Neurolucida file format). Further details are available in this link.

The blender.app Mac OS bundle gives an error when launched from Finder. But it works if the executable is launched from the terminal.

This project would be concerned with all the new feature requests or bugs reported for the Mesh Reconstruction Toolbox panel in NeuroMorphoVis.

To make it sort of complete, it is required to integrate the realistic somata profiles in the MetaObjects. Implementation could be a bit challenging, but it would make a lot of significance for mulitple use cases.

Normal SWC files are assumed to index the samples in an incremental order, for example

2 3 -3.01 -9.03 -18.36 1.005 1
3 3 -3.68 -9.37 -18.36 1.005 2
4 3 -4.01 -10.04 -18.36 1.005 3
5 3 -5.69 -10.71 -18.36 1.005 4
6 3 -6.02 -11.71 -18.36 1.005 5
7 3 -6.69 -12.05 -18.36 1.005 6
8 3 -7.03 -12.38 -18.36 1.005 7
9 3 -7.36 -13.05 -18.36 1.005 8
10 3 -8.03 -13.72 -18.36 1.005 9
11 3 -8.36 -14.39 -18.36 1.005 10
12 3 -8.7 -15.06 -18.36 1.005 11
13 3 -9.37 -15.39 -18.36 1.005 12
14 3 -9.7 -15.73 -18.36 1.005 13
15 3 -10.04 -16.4 -18.36 1.005 14
16 3 -10.71 -16.73 -18.36 1.005 15
17 3 -11.04 -17.4 -18.36 1.005 16
18 3 -11.71 -17.73 -18.36 1.005 17
19 3 -12.04 -18.07 -18.36 1.005 18
20 3 -13.38 -19.07 -18.36 1.005 19

However, SWC files can be manually modified and the order of the indices can change. This issue must be handled, otherwise, the entire morphology skeleton cannot be sketched.

To make the UI less cluttered, replace the thee rendering buttons [Front, Side, Top] by a drop down menu and single button to render the selected view.

• Rendering Option
  ++ Select View [Front, Side, Top] - Render

The current documentation is written in Markdown files. It would be nice to compile it into a PDF as well, upload it to the repository and add another panel in the UI of NeuroMorphoVis to load the documentation directly.

When opening the application, I get the following error message:
“blender” is damaged and can’t be opened. You should move it to the Trash.

Blender itself works from its own download page, but it is not clear how to add the add-on from this repository. Is blender looking for me to point to a .py file that has all the code for the add-on?

This feature is needed to make the terminals realistic or nice looking. Just add a checkbox in the interface.

For consistency, change the order of the Colors & Materials section with the Soft Body Parameters one. The current layout sounds confusing to the testers.

We can use NeuroMorphoVis to load H5 morphologies, visualize them and then we can use move the samples around to manually fix certain artifacts that we cannot be fixed automatically. Therefore, it would be nice to integrate an H5 exporter.

To load any morphology skeleton even if the skeleton is completely messed up, set the default morphology sketching style to Disconnected Segments that does not require computing the angles between the parent and children sections or identifying the short sections.

During the testing phase, I have discovered some morphologies with no basal dendrites. Therefore, we must check if the basal dendrites are None or not before operating on a NoneType.
If this not solved, we will keep getting the following error:

    for dendrite in self.dendrites:
TypeError: 'NoneType' object is not iterable

When we load an SWC morphology file, the last sample in the list is not integrated in the morphology skeleton, and therefore the reconstructed object is not right. This severe issue must be fixed.

I tried to launch NeuroMorphoVis but I received an error message regarding a damaged file when I open Blender.app. (see attachment).

I downloaded the zip file from the MacOS release at:
https://github.com/BlueBrain/NeuroMorphoVis/releases/tag/v1.0.0

When I try to open the blenderplayer.app, it crashes without error message.
My OS: Mojave 10.14.3

(I've downloaded the file multiple times, and always get the same error message).

Change the text on the soma reconstruction button from Soma to Reconstruct Soma

It would be nice to automatically create plots and histograms from the analysis files created from the Morphology Analysis toolbox in NeuroMorphoVis.