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reconstrue / brightfield

Reconstruction of biocytin-stained neurons detected in brightfield microscopy image stacks
http://reconstrue.com
Apache License 2.0
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Circular dendogram ala Hugo #110

Open JohnTigue opened 4 years ago

JohnTigue commented 4 years ago

https://piziadas.com/en/hugo

HUGO (Highly Uniform Graphic Organization) is a software tool; it has been developed to generate graphical representations of neurons stored in Neuromorpho. HUGO is a JAVA based program. In order to run HUGO it is necessary to previously install JAVA’s Virtual Machine, which is available at https://www.java.com/en/download/

Screen Shot 2019-11-24 at 23 02 16

The software is available at https://drive.upm.es/index.php/s/fQjNN5eIn4YN2df

User Manual:

Our software imports the cells, which are stored in a non-proprietary *.swc format.

Screen Shot 2019-11-24 at 23 12 27
JohnTigue commented 4 years ago

Maybe Hugo has a CLI way of being invoked. Then could spin up a JVM on Colav and have it do its thing, i.e. generate a PNG of the SWC as circular dendogram.

JohnTigue commented 4 years ago

Alternatively, just re-impl the paper in Python, e.g. handcoded on stackoverflow.

JohnTigue commented 4 years ago

Or use an existing code such as scipy.hierarchy.dendogram