Improve SVG/PNG export for detailed morphologies in NeuroML2

[pgleeson]

Brief description

An option is available in jNeuroML for quickly converting NeuroML 2 cells into SVG files, which is a quicker way to check/view the structure of cells than loading in OSB 3D Visualiser, neuroConstruct etc. This export requires an update to improve on the basic functionality.

Expected result

The class for generating SVG files from detailed NeuroML2 morphologies is here: https://github.com/NeuroML/org.neuroml.export/blob/master/src/main/java/org/neuroml/export/svg/SVGWriter.java

This is used by jNeuroML to generate a scalable image file using:

jnml L5PC.cell.nml -svg

An example of the current output of this (for a L5 pyramidal cell) is:

This could be improved in numerous ways:

• [x] Improving layout of the 3 side views & fitting them into the print area more compactly
• [x] Add support for networks of cells, e.g. this
• [x] Add (optional) export of colours a/c to whether segments are in soma_group, dendrite_group, axon_group (these names are used for the corresponding segmentGroups)

  Suggested steps

Install jNeuroML from source. Make sure the development branches are checked out (using getNeuroML.py above). Replace the org.neuroml.export with a forked version of this repository Make appropriate updates to SVGWriter.java Note: there is a main() method in that class, but running 'mvn install' will generate an SVG representation of the file L23PyrRS.nml. Issue a pull request for the changes to be checked/merged.

Please do not make extensive changes or reformat large sections of code and expect them to be merged. Please keep changes to a minimum until you let us know about them.

Possible extensions

• [x] Add option to export to PNG files using some standard image processing library (svg->png) available through Maven
• [x] Add off axis view of cell (e.g. looking at 45deg down on cell)

Other detailed morphologies in NML2 are available here for testing: http://www.opensourcebrain.org/search_custom_field?f[]=43&op[43]=~&v[43][]=Detailed+cell+model

Knowledge prerequisites

Java

To be learned

Creating images in SVG Representing morphologies in NeuroML2

Mentor

Contact p.gleeson -at- ucl.ac.uk if you are interested in contributing to this task

[pgleeson]

Currently being worked on by @justasb https://github.com/NeuroML/org.neuroml.export/pull/31 https://github.com/NeuroML/org.neuroml.export/pull/32

[pgleeson]

Significant improvements to this in latest development version of jNeuroML:

Networks also supported:

[pgleeson]

One major addition left, export to PNG...

See convertToPng() method in SVGWriter.java

[pgleeson]

PNG export fixed in latest version