neuromorph-epfl / neuromorph

The NeuroMorph analysis and visualization toolkit

The NeuroMorph Analysis and Visualization Toolkit

This GitHub site provides all NeuroMorph software, datasets, and documentation.

For more information, please visit the NeuroMorph project website.

Documentation

NeuroMorph Wiki ← 🔶 Start Here! 🔶
Detailed instructions for installation and use.

Video Tutorial
Quite legacy at this point, but still helpful for the measurement and image stack interaction tools.

Download

Download a .zip of the full software repository via the green "Code" button above. Or download the .py files of individual tools from their respective folders.

Example meshes, objects, and image files for use with the add-ons can be found in the NeuroMorph_Datasets folder.

Contact

[email protected], [email protected]

neuromorph's Issues

Centerline Processing fails in Blender 3.6.2

Hello,

I am trying to create a centerline on a mesh object that is actually a slightly deformed cylinder, and then I would like to extract the cross-sections. I tried the Neuromorph Centerline Processing plugin in Blender 3.6.2, but I got the following error message:

Python: Traceback (most recent call last):
File "C:\Users*USER*\AppData\Roaming\Blender Foundation\Blender\3.6\scripts\addons\NeuroMorph_Centerline_Processing.py", line 243, in execute
this_area, this_poly = get_cross_section(crv, ind, mesh, kd_mesh, self)
File "C:\Users*USER*\AppData\Roaming\Blender Foundation\Blender\3.6\scripts\addons\NeuroMorph_Centerline_Processing.py", line 1417, in get_cross_section
x = break_code
NameError: name 'break_code' is not defined

I checked the Python script for definitions of break_code and could not find anything. Then I went and tried running the plugin on a simple cylinder mesh. I used the "poke face" command to generate a central point (vertex) on the capping planar faces. Then, I selected the newly created vertices and tried the "Approximate Centerline" command with 10 centerline points. It failed with the same error message. It also created a strange artefact, shown in one of the figures below. The artefact is a new object that was created along with another object (a copy?) of a cylinder (see the screenshot of the model tree below). The only object I had in the tree before was the Cylinder.

Thank you in advance for any help you could provide.

Žiga

Cannot view stack images in Cycles render

Hello,

I am trying to render the stack images using blender cycles. The images display on the plane connected to the stack ladder in the viewport and when I render using Blender Render, however; the plane is blank when I render with Cycles. Any thoughts on how to go about resolving this? I feel like it is something simple, but the solution is eluding me.

Thank you in advance!

Image Flip in Render

My image is flipped in the Render view relative to the Viewport.

Any ideas for troubleshooting?

Thanks!
Sam

Error message when trying to import 3D EM stack

Dear Sirs:
I have been using NeuroMorph for a number of years, and really appreciate the quality of the software.

I have stumbled in an error with a feature I haven't tried before. This is the Display Images from Stack in the 3D drawing function.

I am able to import the stack and create an object called ImageStackLadder with the correct dimensions as shown in this screenshot:

However when I press the Show Images at Vertex bouton I get the following error message:

Any advice?

I am using blender version 2.91.0

Thanks for your help.
Kind regards,
Guilherme

Unable to import images

Hello,

I am trying to import the sample stack of images that were posted in the Data directory, however it is throwing me a weird error. Here is step by step what I am doing.

1. I first opened up the blender file that I downloaded from this repository:
   

2. Then I selected the directory that I wanted to be the source of the Z-source port
   

3. I selected the folder and it returned to the 3d view, now with the red stack ladder present.
   

4. Finally to visualize the images I hit the button 'Show Images(s) at Vertex' and it gave me the following error shown in the image below
   

Any thoughts on why this is happening?

Thank you!