The general working principle of GEPARD is explained herein.
Setup the gepard.cfg
For optimal use, please create a copy of the
sample_gepard.cfg and rename it to
gepard.cfg. Within this config-file, a default file path and the Raman Control Interface that shall be used is defined. Further (microscope specific) options can be defined as well.
In default configuration GEPARD will use the SIMULATED_RAMAN interface. This means that no microscope is connected and all control instruction such as moving the specimen table are basically non-operations. Also images are taken from a single default picture only. This interface is used for testing. For real sample analysis select an interface such as the WITec interface in the config-file.
Using GEPARD with WITec Raman microscopes
As long as you don't do anything with your WITec software GEPARD won't be able to interfere with the microscope. Gepard itself is not able to directly connect to the Raman microscope and uses for example WITec-Control for this purpose. This remote access needs to be actively enabled in the WITec Control software.
Make sure that you have at least Version 5.0 of WITec-Control installed. In versions prior to 5.1 activate Default Tree mode (right click in the left control panel). Then activate "Allow Remote Access". This remote access can be revoked at any time with a large button in WITec Control. After the access is denied again your WITec Control should run as before. Now, try the witectest.py sample first with objectives turned away from the samples to avoid damage by uncontrolled movement.
To activate the WITec backend for GEPARD set the 'raman_interface' variable to 'WITEC_CONTROL' in
gepard.cfg. Restart GEPARD to activate the new configuration. If GEPARD is still running with the simulated interface this fact will be shown in the window title. If the WITec interface import fails for example due to missing win32com packages GEPARD will still use the simulated interface. If you forgot to allow the remote access before starting GEPARD you have to manually connect GEPARD by clicking
Connect to Microscope after allowing the remote access in WITec Control.
Creating and performing a measurement
After starting the GEPARD, a new measurement can be created by hitting the "New Measurement"-Button. A prompt window asks for a project name. GEPARD will create a directory with this name and save all required data within this folder. A project file will be saved as well, currently implemented by using the python pickle module. While conducting the experiment, GEPARD leads the user through the following steps, as also indicated in the toolbar-menu on the left-hand side of the program:
- Optical Scan: Acquire a stitched image with focus-stacking
- Particle Detection: Detect particles by watershed image-segmentation. A number of adjustable parameters is provided for controlling the detection result.
- Raman Scan: Measure all particles with defined Raman conditions.
- Particle Analysis: Load spectra and analysis results from external program and review particle statistics.
A detailed description of every step can be found on the respective wiki Page.