Windows issues

We have a few interns working on NeuroML projects and a few of them that use Windows as their primary operating system have reported issues on installing/using various bits of the NeuroML stack. Unfortunately, none of us on the NeuroML developer team use Windows, so we haven't run into these issues and they're harder for us to fix.

Generally, installing the basic bits of the NeuroML stack on Windows is not too hard. One needs to have a functioning Java Runtime Environment (JRE) along with a Python installation. Both of these aren't very hard to install, since installers for Windows are readily available.

From then on, one only needs to set up a virtual environment and install pyNeuroML using pip. This pulls in all the Python dependencies, and we also bundle the necessary Java bits with it.

Other optional dependencies, though, can be tricky. For example, one can install NEURON on Windows using the installer they provide, however, one also needs to have a compiler tool chain to use NEURON, and that isn't necessarily straightforward. I still don't know how this is to be set up correctly.

Next, a few folks have reported issues getting our Vispy based visualization code to run on Windows. Vispy requires a backend to run, like Qt5 or Qt6, so one has to make sure these work on their Windows installs to use Vispy.

The Windows Subsystem for Linux is something lots of Windows users now use. It's great for development, but GUI elements don't seem to work on it out of the box (from what I hear).

Using SWC morphology files

Screenshot of NeuroMorpho.org

SWC is a specification/format used to store reconstructions of biological entities, like neurons. It's commonly used in various places like on https://neuromorpho.org, a database of neuronal reconstructions.

A use-case that NeuroML needs to support is the use of these reconstructions in models. Of course, these reconstructions are not always made for use in models, so they can have various issues that need to first be corrected. We have a page on these in the docs.

A few tools do allow the semi-automated conversion of SWC morphologies to NeuroML. CVApp is one such tool. We made some updates/fixes to it this week to ensure it works correctly, and also updated the documentation to add a page dedicated to the conversion of SWC to NeuroML.

We also support storing these NeuroML morphologies in separate files now, and I updated pyNeuroML to also visualise these using our Vispy viewer

Google Summer of Code

I merged Ioannis's PR that included tweaks to our 3D visualiser to make cells look "upright". I also made some other tweaks to it to show the X, Y, Z, axes with the plots and improve the camera view. Ioannis is now looking into making our visualisations work in Jupyter notebooks.

I reviewed Aditya's PR and gave some feedback. He's made his changes now, and I've got to do another review, hopefully tomorrow. In the meantime, Aditya is playing with CVApp and other tools to gain a better understanding of the SWC to NeuroML conversion process.

Paper review responses

We worked on replying to the reviewers' responses on our submission to E-Life. We hope to send the updated version back in this week. This took quite a while.