README

# SPEKcheck

SPEKcheck is a web application to visualise the efficiency of the
light path in a fluorescence microscope.  It can run locally and
completely offline, or it can be configured to run in a site.

SPEKcheck models an optical setup as a detector, a dye, an excitation
source, and an arbitrary number of filters in both the excitation and
emission paths.  SPEKcheck then reports values for the excitation
efficiency of the dye, the collection efficiency of the emitted
fluorescence, and a 'brightness' score, all easy comparison between
different fluorescent labels.  It also displays a spectral plot of
various components, and the final emitted fluorescence.

## Trying SPEKcheck

A public of instance is available online at
https://www.micron.ox.ac.uk/software/spekcheck

## Documentation

A manual with configuration and installation options is included in
the release.  It is also available online at
https://www.micron.ox.ac.uk/software/spekcheck/help.html

## Installation

1. Download the latest release from the releases page:

    https://github.com/MicronOxford/SpekCheck/releases/

2. SPEkcheck can then run in two modes:

   1. To run without a web server, simply open the `index.html`.
    Browsers other than Firefox will require extra configuration to
    run it this way, see `help.html` for details.

   2. To run with a web server, move the SPEKcheck directory into
    whatever directory your web server is configured to serve.
    Alternatively, run `python -m SimpleHTTPServer` and then connect
    to http://127.0.0.1:8000/index.html