Package: neuromynerva
Get Started|Full FlyBrainLab Install|Installation JupyterLab 3.x|Develop JupyterLab 3.x|Installation JupyterLab 2.x|Develop JupyterLab 2.x|Getting helpNeuroMynervav2-FlyBrainLab's JupyterLab ExtensionNeuroMynerva V2 is currently inalpha, most main user-facing features have been implemented but we expect bug fixes and additional features to be incorporated in the near future. If you want to report a bug, please seeGetting Help. To follow the latest developments on this project, follow the Fruit Fly Brain Observatory(FFBO)Twitterwhere we post weekly updates.Get StartedNote:Following JupyterLab 3.0's new extension system, NeuroMynerva is now distributed
on PyPI and can be installed using your python installer.
Please follow installation instruction detailed inInstallationsection
for details on how to install and/or develop NeuroMynerva.Using NeuroMynerva and FlyBrainLabThe best way to get started with NeuroMynerva is to look at the instructions on theFlyBrainLab's pageand theWikitherein.For developers interested in the technical aspects of the NeuroMynerva platform, you can refer to theNeuroMynerva Wiki.Key ComponentsNeuroMynerva front-end currently includes 4 key components:Neu3D-Widget: A neuron/synapse morphology visualization toolkit that supports 3D rendering of neuron skeletons and meshes.Info-Widget: A side panel widget that shows detailed neuron information (metadata, pre-/post- synaptic partners, etc.). Content updated by clicking on individual neurons inNeu3D-Widget.NeuGFX-Widget: A circuit visualization widget.Master-Widget: A side panel widget that keeps track of all currently running NeuroMynerva widgets.InstallationPrerequisitesNeuroMynerva has the following requirements:Python Version 3.6+JupyterLab >= 2.2.0 or JupyterLab >= 3.0.0JupyterLab 2.x and 3.x have different installation instructions.
See the sections below (Jlab 2.x,Jlab 3.x)Packages:Neuroballadand packages required therein,flybrainlaband packages required therein.1. Installation of Full FlyBrainLab Eco-SystemUp-to-date installation instructions for the whole FlyBrainLab ecosystem
(NeuroMynerva + FlyBrainLab User-side and Server-side Backends)
are available athttps://github.com/FlyBrainLab/FlyBrainLab#readme.2. Install/Develop/Uninstall onJupyterLab 3.xInstallation of NeuroMynervaJupyterLab 3.x supports installing NeuroMynerva as a python package.
You can install NeuroMynerva directly from PyPI via command line aspipinstallgit+https://github.com/mkturkcan/autobahn-sync.gitgit+https://github.com/FlyBrainLab/Neuroballad.gitgit+https://github.com/palash1992/GEM.gitgit+https://github.com/mkturkcan/nxcontrol# flybrainlab requirementspipinstallflybrainlab# required package for communicating with backendpipinstallneuromynerva# and refresh browser afterwardsDevelop NeuroMynervaWe useAnacondato manage development environment, you are encouraged to first create a Conda environment# create conda environment and install python dependenciescondacreate-nfblpython=3.7nodejsscipypandascookiecuttergityarn-cconda-forge-y
condaactivatefblYou can then use the following script to setup the development environment.# create conda environment and install python dependenciespipinstalljupyterjupyterlab>=3pipinstalltxaiotwistedautobahncrochetservice_identityautobahn-syncmatplotlibh5pyseabornfastclusternetworkxmsgpackjupyter-packaging# if on Windows, execute the following:# pip install pypiwin32# Install flybrainlab package for communication with backendpipinstallflybrainlab# Alternative, you can download the source code for the inhouse packages as well# git clone https://github.com/FlyBrainLab/Neuroballad.git# git clone https://github.com/FlyBrainLab/FBLClient.git# cd ./Neuroballad# python setup.py develop# cd ../FBLClient# python setup.py developNext, we build the NeuroMynerva from source.Note:You will need NodeJS to build the extension package.Thejlpmcommand is JupyterLab's pinned version ofyarnthat is installed with JupyterLab. You may useyarnornpmin lieu ofjlpmbelow.# assuming currently in FBLClient foldercd../# go back to parent folder on the same level as FBLClient and NeuroBallad# Clone the repo to your local environment# Change directory to the neuromynerva directorygitclonehttps://github.com/FlyBrainLab/NeuroMynerva.gitcd./NeuroMynerva# Install package in development modepipinstall-e.# Link your development version of the extension with JupyterLabjupyterlabextensiondevelop.--overwrite# Rebuild extension Typescript source after making changesjlpmrunbuildYou can watch the source directory and run JupyterLab at the same time in different terminals to watch for changes in the extension's source and automatically rebuild the extension.# Watch the source directory in one terminal, automatically rebuilding when neededjlpmrunwatch# Run JupyterLab in another terminaljupyterlabWith the watch command running, every saved change will immediately be built locally and available in your running JupyterLab. Refresh JupyterLab to load the change in your browser (you may need to wait several seconds for the extension to be rebuilt).By default, thejlpm run buildcommand generates the source maps for this extension to make it easier to debug using the browser dev tools. To also generate source maps for the JupyterLab core extensions, you can run the following command:jupyterlabbuild--minimize=FalseUninstallpipuninstallneuromynerva3. Install/Develop/Uninstall onJupyterLab 2.xInstallation of NeuroMynervaJupyterLab 2.x requires installing NeuroMynerva as an NPM pacakge.
You can install NeuroMynerva directly from NPM via command line aspipinstallflybrainlab# required package for communicating with backendjupyterlabextensioninstall@flybrainlab/neuromynervaDeveloping NeuroMynervaWe useAnacondato manage development environment, you are encouraged to first create a Conda environment# create conda environment and install python dependenciescondacreate-nfblpython=3.7nodejsscipypandascookiecuttergityarn-cconda-forge-y
condaactivatefblYou can then use the following script to setup the development environment.# create conda environment and install python dependenciespipinstalljupyterjupyterlab==2.2.9
pipinstalltxaiotwistedautobahncrochetservice_identityautobahn-syncmatplotlibh5pyseabornfastclusternetworkxmsgpack# if on Windows, execute the following:# pip install pypiwin32# install inhouse packages and NeuroMynervagitclonehttps://github.com/FlyBrainLab/NeuroMynerva.git
gitclonehttps://github.com/FlyBrainLab/Neuroballad.git
gitclonehttps://github.com/FlyBrainLab/FBLClient.gitcd./Neuroballad
pythonsetup.pydevelopcd../FBLClient
pythonsetup.pydevelopcd../NeuroMynerva
jlpm
jupyterlabextensionlink.# # watch for source code changes in NeuroMynervajlpmrunwatch:src# in a separate terminaljupyterlab--watchUninstalljupyterlabextensionuninstall@flybrainlab/neuromynervaGetting HelpThe best way to get help right now is tosubmit an issue.
You can also join ourGitterand ask us questions there.