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Density visualization plugin for neuronal morphologies

Home Page: http://www.neurobox.eu

License: Artistic License 2.0

Java 99.31% TeX 0.69%

swc java vrl-plugin density-visualization vrl-studio neuronal morphologies

vrl-swc-density-vis's Introduction

VRL-SWC-Density-Vis

A VRL Studio plugin for the density visualization and subsequent analysis of stacks of neuronal morphologies specified in the common SWC file format (cf. neuromorpho database) compatible with e. g. Neurolucida, NEURON or GENESIS. By extending the existing VRL-Density-Vis plugin for the matter in hand, the VRL-SWC-Density-Vis plugin integrates flawless within the novel NeuroBox 3D toolbox for detailed simulations and analysis in Computational Neuroscience (compare the organization NeuroBox3D). For a specification of the SWC file format cf. NeuroLand.

CI and license

Literature

You are obliged to cite the following reference (See in Bibtex format here) if you use the software to analyze and publish results: Grein Stephan, Qi Guanxiao, Queisser Gillian (2020): Density Visualization Pipeline: A Tool for Cellular and Network Density Visualization and Analysis in Frontiers in Computational Neuroscience for From Neuronal Network to Artificial Neural Network: Structure, Function and Intelligence

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vrl-swc-density-vis's Issues

Add factory methods for matrices

The matrix functionality has to be refactored into another plugin, e.g. Utils Plugin, since this is useful not only in the VRL-SWC-Density-Vis plugin.

introduce return type descriptions for components

Add unit tests for the new VRL type representations.

Implement Sparse Matrix and Sparse Vector on the basis of the Sparse Matrix

... and then factor out of this Plugin.

Immediate TODOs

cf. Commit, then remaining issues.

Coarsen the consensus geometry if >500,000 cylinders/triangles in input file

Remove duplicated code

... and cleanup code.

3D density maps without and with gaussian blurring

Add license

Enhance README and reference to paper

Add contours to Impl and speedup DiamImpl

The scale bar placement has to be improved (and the scaling of the scale bar itself).

Validate computeDensity

Data projection to a given plane

Navigate by ARROW keys through geometry

Improve rotational view (Export movie), scale bar and axes placement.

Needs fine-tuning.

Generalize BasicMatrix2D TypeRepresentation

Generalize BasicMatrix2D TypeRepresentation (DenseMatrix and SparseMatrix) by DenseMatrixBaseType and SparseMatrixBaseType, we register also some components like Dense2x2Matrix, but in general one wants to write code with @paraminfo(options="cols=3; rows=4" etc... also in Groovy Code Template would be nice to know how to add

Refactor and create public interface for the density computation

add description and tooltip strings

TODOs for publication (iss33)

~~1. Project 3D density data to 1D axes, e.g. x axis, y axis and z axis~~
Minor:
~~2. Fix schematic XML density visualizer: Contours might not be present. Speedup cylinder strategy~~
~~3. Test new template project for projection to axes~~
~~4. Fix DensityVisualization VRL component to produce correct number of cuboids for plotting~~
Major:
~~5. Show functionality as described by GQ's paper suggestion and Box and Dropbox folder Illustrations~~

Filter out common components for NeuroBox

Add vol of frustum

Addressed.

Select compartments which should be visualized

Documentation for Plugin

Use the explanations from

https://github.com/VRL-Studio/VRL-Studio/wiki/How-to-Create-Documentation-for-VRL-Studio-Plugins

to include documentation for this plugin.

Density

The density does not respect the sampling cube size, but this should be the case.

Scale geometry and remove colors

DenseMatrixArrayType does not respect ParamOptions

Implement computeDensity alternative

computeDensity must respect the compartment type selection

Benchmarking

BasicMatrix1D TypeRepresentations as DenseVector respectively SparseVector

Visualization

Migrate from Java3D to JavaFX3D.

Introduce compartment type selection

Enables to select only e. g. axons, dendrites, etc of the geometry instead of all compartment pieces.

computeDistance

This should be implemented in DistanceImpl accordingly.
Do we just plot the edge distribution?!

Further todos

See meeting details, since this is confident

Add contours to DensityVisImpl as LineArray and Marching Cubes scaling

Add possibility to display ALL geometries instead of one consensus geometry

3D density maps with isosurfaces and normals

Use marching cubes on the density data (voxels) to extract iso surfaces.
Need to calculate normals too to provide illumination model.

Migrate to JavaFX

Implement Shape3DArrayCustom based on HashMap<String, Shape3D> for easier access.

TODOs from code and merge iss33 into devel branch

There is an assortment of minor TODOs distributed within the codebasis.
These have to be ALL addressed for the next milestone v.2.0.

Refactor all System.* print statements to use a Log4J to prepare for release.

Furthermore, after addressing iss33, which will fix all issues for milestone v1,
the code will be merged back to the devel branch. From the devel branch
another feature branch (milestone v2) will be created to address the milestone.

If all tests work, devel branch will be next merged back into master branch,
before addressing milestone v2.