Algorithm Protocols
Algorithms are defined sequences of actions to be performed by the IC200 instrument. These protocols are generally tailored to a specific biology or assay. Algorithms know the fluorescent excitation light source, autofocus method(s), emission filters and camera settings needed for an assay. Defaults for excitation light source, light source intensity, integration time, gain and binning are set here but can be modified at the time of scan.
Create, modify or delete an algorithm protocol via the 'File --> Edit Algorithms' command.
Select Algorithm to modify. Note that all algorithms can be duplicated or deleted. New algorithms can be created but the fastest way to build new algorithms is to duplicate an existing algorithm.
Note that the highlighted channel in the left panel has corresponding settings in the right panel. Acquire settings to change are in the 'acquireSettingsInfo' section. The 'lightSourceInfo' and 'cameraSettingsInfo' sections are where most of the changes are needed.
Entries in the right panel can be updated by triple clicking the item. Once the edit is complete, press enter. Once a number of settings are in place, click 'Apply' and then 'Save Changes'. This will update the file so that it is available throughout the rest of the program. The 'Show Types' and 'Show Descriptions' checkboxes are very helpful for finding detailed information and units.
This table describes the standard excitation/emission set. The (colors) in parenthesis correspond to the colors in the 'Channel Settings' dialog. The numbered sequence indicates the standard filter wheel position associated with each excitation. When editing an algorithm, emission filters should have the form 'Filter 4'. Some fluorophores may require custom matching of excitation light source and emission filter wheel position.
Some system configurations may vary.
Standard systems ship with 2 filter cubes. This is the spectra for cube 1.
Standard systems ship with 2 filter cubes. This is the spectra for cube 2.
CyteSeerReader saves all software configurations and algorithm protocols in XML files. The problem literally reads in the appropriate XML file before scanning to set up the parameters of the scan.
This is a small section of the text from within an algorithm XML file. Editing these files directly is not recommended. This section is shown as an example to help describe the system architecture. The architecture is built from the ground up to be flexible to changing hardware and graphical user interfaces. There is a lot of detail built into these algorithms. Sophisticated options for time series, z-stacks and higher speed video rate acquisition are covered in another lesson.
