Scanimage 2017 : Configuring Photon Counting Modules


This feature is only available with the Resonant Scanning imaging system.


ScanImage 2016 can use photon counting modules instead of standard PMTs. A photon counting head / module consits of a PMT and a subsequent photon counting circuit. This circuit generates a TTL pulse of a defined duration when a photon is detected. ScanImage samples this TTL pulse using the auxiliary digital inputs PFI0-3 of the NI 573x digitizer modules.


To configure photon counting for ResScan, add the following entries to the Machine Data File:

%% ResScan
% the features 'Aux Triggering' 'I2C' and 'Photon Counting' are mutually exclusive
I2CEnable = false;
auxTriggersEnable = false;
photonCountingEnable = true; % enable photon counting feature
photonCountingDisableAveraging = true; % disable averaging of samples into pixels; instead accumulate samples
photonCountingScaleByPowerOfTwo = 0;   % if photonCountingDisableAveraging == false scale count before averaging to avoid loss of precision by integer division
photonCountingDebounce = 0; % [s] time the TTL input needs to be high before a pulse is registered

The setting photonCountingDebounce can be used to clean up a noisy signal. The delay introduced by photonCountingDebounce can be eliminated by adjusting the value for the scan phase in Configuration Controls.



To be detected by the digitizer, the duration of the pulse output by the photon counting module needs to be longer than the sample period of the digitizer module. See the list below for the sample duration of digitizers typically used with ScanImage.

DigitizerSample RateMinimum Pulse
NI 573280 MHz12.5 ns
NI 5733120 MHz8.4 ns
NI 5734120 MHz8.4 ns

Photon Counting Modules cannot discriminate multiple photons arriving in a small time interval. After a photon arrives, the photon counting circuit outputs a high pulse followed by a low signal of a specified duration. During this output time, the photon counting circuit ignores all photons arriving at the PMT.

This makes photon counting modules only suitable for applications where a low photon rate is expected.

Wiring for Photon Counting Modules


Photon Counting Modules that output a TTL pulse for each detected photon are connected to the digital I/O port on the NI573x digitizer module using a NI SCB-19 breakout box.