ContentMine/neuro

Name: neuro

Owner: The ContentMine

Description: Neurophysiology, especially voltage traces

Created: 2015-10-11 17:50:31.0

Updated: 2016-11-08 08:52:25.0

Pushed: 2015-10-11 18:48:00.0

Homepage: null

Size: 121

Language: null

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README

neuro

Neurophysiology, especially voltage traces Primarily to scrape images of voltage/current plots and analyze them semantically.

The whole project is run as Open NotebookScience https://en.wikipedia.org/wiki/Open_notebook_science and everything should either be in this repo or accessible from it.

• Raw data will be stored in this repo. (Copyrighted material may be omitted).
• IPython (Jupyter) will be used as the primary recording mechanism
• analysis software (e.g diagramanalyzer will be modified to create log files which will be posted alongside the computed data

Currently the analysis software is in https://bitbucket.org/petermr/diagramanalyzer/ - see NeuroAnalyzerTest for the latest prototype.

There is a scraper for J. Neuroscience in jneuro.json . First you need to create a list of URLs. @blah404 will create a quickcrawl but until then:

enter a search in J.Neurophysiology using Firefox (because the HTML will be different elsewhere - this is a temporary hack until quickcrawl). Typical:

://www.jneurosci.org/search?fulltext=CA1+and+pyramidal+and+clamp&submit=yes&x=9&y=10&hits=200

This will run the search for “CA1” and “pyramidal” and “clamp” and output <= 200 hits in a single HTML file. To extract the URLs on a UNIX commandline:

This should create urls.txt (else find a UNIX guru and buy them a drink).

To run the scraper:

kscrape --urllist urls.txt --scraper ../../journal-scrapers/scrapers/jneuro.json --output ca1 --loglevel verbose

where ca1 should be renamed to your output directory (CProject) and the logging level can be reduced.