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

### Download node.js files and setup indices.

You will likely need to run make to install the required npm packages,
generate help files and generate the required json indices of
filters, dyes, excitation sources and detectors. On a unix like system
(Linux or macos) this can likely be done by running 'make' at the
command line.

### Likely needed steps on Windows

On windows this is more involved due to the lack of a number of the
expected packages. The easiest way to solve this is to use WSL (the
windows system for Linux) to run the linux tools directly on
windows. this involves a few steps.

1) Install WSL: Start a command prompt from the start menu and type
'wsl'. This will run wsl if it is installed or prompt you on how to
install it if it isn't.

2) Install make sudo apt install make

3) Install npm by following the instructions on
https://learn.microsoft.com/en-us/windows/dev-environment/javascript/nodejs-on-wsl

but I managed with

 curl -o-
 https://raw.githubusercontent.com/nvm-sh/nvm/master/install.sh | bash

wait while that installs, then you need to restart your shell or
otherwise execute your startup script as it alters your path. I
rexecuted my startup script with

 source ~/.bashrc

Then install the latest long term support version of the tools with 

 nvm install --lts

That actually installs npm which make will use to install the required
node.js libraries

4) Install a couple of graphics tools for the help files
First to get rsvg-convert

 sudo apt install librsvg2-bin

Then to get icotool

 sudo apt install icoutils

5) Then to download and install the js packages, generate web
pages,help files and json indices.

make

The package should now work.