Merge pull request #392 from Hjorthmedh/region_mesh_redux

Bending morphologies that approach the edge of the volume.

examples/notebooks/README.md

@@ -10,6 +10,7 @@ Here is a collection of Jupyter Notebooks, some of the workflows are split over
 * [population_unit_network](population_unit_network.ipynb) how to define population units.
 * [example_of_density_function](example_of_density_function.ipynb) how to specify density variations using a function of (x,y,z) in a volume.
 * [example_of_neuron_rotations](example_of_neuron_rotations.ipynb) shows how to rotate neurons based on position.
+* [bend_morphologies](bend_morphologies.ipynb) shows how to make the neurons bend the axons and dendrites at the edge of the mesh, to keep them constrained to the volume.
 * [connect_structures_example](connect_structures_example.ipynb) shows how to create neuron projections between volumes when no-axon data is available ([parallel version](connect_structures_example_parallel.ipynb)). There is also an [alternative version](connect_structures_example_projection_detection.ipynb) that places axon voxels randomly within the projection zone and then applies touch detection.
 * [virtual_neurons](VirtualNeurons/VirtualNeurons.ipynb) shows how to only simulate the core of a volume of neurons, by turning the outer neurons to virtual neurons that spike at predetermined times. This is useful to avoid edge effects in your simulations.
 

requirements.txt

@@ -16,6 +16,7 @@ setuptools
 psutil >= 5.8.0
 cython  # Needed for compiling NEURON
 wheel  # setup.py seems to need this now
+open3d
 
 # igraph
 # snudda

snudda/__init__.py

@@ -1,6 +1,6 @@
 from .core import Snudda
 
-__version__ = "1.4.73"
+__version__ = "1.5.0"
 
 from .init import SnuddaInit
 from .place import SnuddaPlace