https://github.com/rossant/spiky

THIS REPOSITORY IS OUTDATED, the new one is:
https://github.com/rossant/spiky

Last synced: 14 days ago
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THIS REPOSITORY IS OUTDATED, the new one is:

• Host: GitHub
• URL: https://github.com/rossant/spiky
• Owner: rossant
• License: other
• Created: 2012-10-22T08:44:56.000Z (about 13 years ago)
• Default Branch: master
• Last Pushed: 2013-04-29T13:00:48.000Z (over 12 years ago)
• Last Synced: 2025-01-20T23:28:15.320Z (12 months ago)
• Language: Python
• Homepage: https://github.com/klusta-team/klustaviewa
• Size: 3.9 MB
• Stars: 2
• Watchers: 4
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.md

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README

          
## THIS REPOSITORY IS OUTDATED

[The new repository can be found here.](https://github.com/klusta-team/klustaviewa)

## Old notes

*Spiky* is the code name for the next-generation spike-sorting software 

adapted to high-channel count silicon probes. Written in Python, it aims at 

being flexible and extendable by the user.

The first step is to create a new semi-automatic graphical interface

(code name: *KlustaViewa*) for

the manual stage that comes after the automatic clustering algorithms.

This interface automatically guides the user through similar clusters,

showing the most relevant feature projections, and asks him or her to make merge or

split decisions. The goal is to make the manual stage more reliable, less

error-prone and quicker than what it currently is.

This software was developed by Cyrille Rossant in the [Cortical Processing Laboratory](http://www.ucl.ac.uk/cortexlab) at UCL.

Installation

------------

The software is still in development, but you can download an experimental

version here.

### Step 1

If you don't already have a Python distribution, install [Enthought Python Distribution](http://www.enthought.com/products/edudownload.php) (EPD), which is free for academics (*EPD ACADEMIC SUBSCRIPTION* and **NOT** *EPD FREE*).

You need to click on *request an academic license here* on the webpage and create an account with your **academic e-mail address**.

### Step 2

[Download Spiky](http://spiky.rossant.net/spiky-0.1.0.dev.zip)

### Step 3

Extract this ZIP file in a temporary folder.

### Step 4

  * On Windows, double-click on `windows_install.bat`.

  * On other systems, open a system shell in the temporary directory where

    you extracted the package, and execute the following command:

    `python setup.py install`.

### Step 5

To run the software, execute `spiky` in a system shell.

On Windows, you may need to add `C:\Python27\Scripts` in the PATH variable,

as [described here](http://geekswithblogs.net/renso/archive/2009/10/21/how-to-set-the-windows-path-in-windows-7.aspx).

Gallery

-------

[![Screenshot 1](images/thumbnails/img0.png)](images/img0.png)

[![Screenshot 2](images/thumbnails/img1.png)](images/img1.png)

[![Screenshot 3](images/thumbnails/img2.png)](images/img2.png)

Installation for advanced users

-------------------------------

### Dependencies

  

The following libraries are required:

  

  * Python 2.7

  * Numpy

  * Pandas >= 0.10

  * Matplotlib >= 1.1.1

  * PyOpenGL >= 3.0.1

  * either PyQt4 or PySide

There are two possibilities to install these dependencies.

  

#### Use an all-in-one Python distribution

All these dependencies are included in the 

[Enthought Python Distribution](http://www.enthought.com/products/epd.php) (EPD),

which is free for academics.

#### Install all packages one by one

This solution can be useful if you already have a Python installation and 

only a few packages are missing.

  * On Windows, [find the packages on this webpage](http://www.lfd.uci.edu/~gohlke/pythonlibs/).

  * On OS X, find them on [Homebrew](http://mxcl.github.com/homebrew/) or [Macports](http://www.macports.org/)

  * On Ubuntu, use `apt-get install` with the appropriate package name, which you can find [here](http://packages.ubuntu.com/):

        

        sudo apt-get install python-numpy python-pandas python-matplotlib python-opengl python-qt4 python-qt4-gl

### Installer

[Download Spiky](http://spiky.rossant.net/spiky-0.1.0.dev.zip), extract that package

and execute `python setup.py install`.

### Development version

Use this if you want to be able to update with `git pull` (you need git).

  * Clone the repository:

  

        git clone https://github.com/rossant/spiky.git

  

  * Install Spiky with `pip` so that external packages are automatically

    updated (like `qtools` which contains some Qt-related utility functions):

  

        pip install -r requirements.txt