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Nemaload Logo #NEMASHOW NEMASHOW is a web application which enables the public to access interactive visualizations of data produced by the NEMALOAD project. Nemashow is built on the Meteor framework, and uses WebGL for visualizations.

##Datasets NEMASHOW allows you to explore snapshots and videos capturing c. elegans specimen on microscopic scale. But 2D images are not enough for us - we are looking for ways to achieve a 3D capture of the worm's neuronal activity. We offer two kinds of data - "light field" data that uses clever optics to capture the worm's body from multiple angles simultaneously and "light field" data (still experimental) that uses laser scanning to capture a fully 3D model.

For the light field data, we also already offer some very simple data visualization. This is still a work in progress though, so please consider the visualized data (neuron positions etc.) as just a demo.

##Technical Setup ###Overview The process of getting a working copy of NEMASHOW can be grouped into several broad steps:

  1. Ensuring your setup meets the necessary requirements and has the necessary dependencies
  2. Downloading the repositories and, optionally, the project dataset
  3. Running setup scripts

###Requirements ####Browser A WebGL capable browser is necessary to view the visualizations(we use the latest Chrome builds; you can test your browser here.) Support for other browsers is not guaranteed.

####Operating System #####Running NEMASHOW In production, NEMASHOW runs on servers running Ubuntu 13.04. However, development takes place on other Linux distributions, as well as Mac OS X.

#####Viewing NEMASHOW Usually, if a WebGL capable browser can be successfully installed and tested, NEMASHOW will work.

One notable exception is light-sheet visualizations with the prerelease version of Mac OSX 10.9, due to a strange bug involving Cross Origin Resource Sharing. However, this OS version can be used when the light-sheet images and web app are hosted on the same server.

####Storage Space If you'd like to store the raw dataset, ~30GB of space is necessary. To store the PNG renderings of the files, ~7GB is necessary.

###Dependencies ####Meteor The easiest way to install Meteor is to run the command $ curl https://install.meteor.com | sh on a supported platform.

####Meteorite We use several Meteorite packages in the NEMASHOW application. This package is best installed with npm using the command npm install -g meteorite.

####MongoDB The MongoDB command line tools are necessary to run some setup scripts.

####Python Libraries If you choose to run the HDF server or computation server, several Python libraries are required as well as their various dependencies, including:

  • Tables
  • MatplotLib
  • SciPy

###Data ####Database Meteor will automatically generate the necessary collections the first time it runs. However, to import the information about our dataset, you can use the monogorestore command on the database dump in /meteor/dump/.

####Dataset The application expects to find data in meteor/data (absent from this repository). The actual dataset is many gigabytes; please contact us if you'd like a copy.

###Usage

To run the website, run the mrt command from the meteor directory and point your browser at http://localhost:3000/. To access lightsheet images data, you also need to run the ./simple-hdf-server.py ../data command, where ../data is the directory holding HDF5 lightsheet data files. To access lightsheet bounding box plotting functionality, also run the ./computation-server.py ../data command.

###Administration To make a user an administrator, direct database access is required. In the db.users collection, simply set a user's admin field to "admin".

##Roadmap NEMASHOW will continue to grow as the project does. As the project continues in its analysis of and signal extraction from the datasets, additional features will be added to the visualization to reflect this progress.

License

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.