Time-Resolved Fluorescence Wiki

pre-histogrammed_image

Anonymous (anonymous@undisclosed.example.com) — 2023-11-15T14:13:50+00:00

2016/03/03 09:58		current
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	====== Structure of the pre-histogrammed Image Data File======		====== Structure of the pre-histogrammed Image Data File======
-	****	+
	^Data Item ^^^^Type ^Description ^		^Data Item ^^^^Type ^Description ^
	\|PixX \|\|\|\|''int32'' \|pixels in X-direction \|		\|PixX \|\|\|\|''int32'' \|pixels in X-direction \|
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-	For an example in python see here: https://github.com/PicoQuant/pre-histogrammed-Image-Data-File	+	For an example in Python and Matlab see here: https://github.com/PicoQuant/pre-histogrammed-Image-Data-File

t3-mode

Anonymous (anonymous@undisclosed.example.com) — 2015-02-10T16:27:57+00:00

2015/02/10 16:26		current
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	- the arrival time of the event pair on the overall experiment time scale (the time tag).		- the arrival time of the event pair on the overall experiment time scale (the time tag).

-	The latter was originally obtained from an independent asynchronous clock. This made it difficult to combine the start-stop timing with the time tag or to know the sync period the event belonged to. For the PicoHarp's T3 Mode a smarter approach was chosen:\\	+	The latter was originally obtained from an independent asynchronous clock. This made it difficult to combine the start-stop timing with the time tag or to know the sync period the event belonged to. For the *Harp's T3 Mode a smarter approach was chosen:\\
	The time tag is now obtained by simply counting sync pulses. From the T3 Mode event records it is therefore possible to precisely determine which sync period a photon event belongs to. Since the sync period is also known precisely, this furthermore allows to reconstruct the arrival time of the photon with respect to the overall experiment time.		The time tag is now obtained by simply counting sync pulses. From the T3 Mode event records it is therefore possible to precisely determine which sync period a photon event belongs to. Since the sync period is also known precisely, this furthermore allows to reconstruct the arrival time of the photon with respect to the overall experiment time.

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	If the counter overflows, a special overflow marker record is inserted in the data stream, so that upon processing of the data stream a theoretically infinite time span can be recovered. The 12 bits for the start-stop time difference cover a time span of 4096*R where R is the chosen resolution. At the highest possible resolution of 4 ps this results in a span of 16 ns. If the time difference between photon and the last sync event is larger, the photon event cannot be recorded. This is the same as in histogramming mode, where the number of bins is also finite. However, by choosing a suitable sync rate and a compatible resolution R, it should be possible to reasonably accommodate all relevant experiment scenarios. R can be chosen in doubling steps between 4 ps and 512 ps.		If the counter overflows, a special overflow marker record is inserted in the data stream, so that upon processing of the data stream a theoretically infinite time span can be recovered. The 12 bits for the start-stop time difference cover a time span of 4096*R where R is the chosen resolution. At the highest possible resolution of 4 ps this results in a span of 16 ns. If the time difference between photon and the last sync event is larger, the photon event cannot be recorded. This is the same as in histogramming mode, where the number of bins is also finite. However, by choosing a suitable sync rate and a compatible resolution R, it should be possible to reasonably accommodate all relevant experiment scenarios. R can be chosen in doubling steps between 4 ps and 512 ps.

-	Dead time in T3 Mode is the same as in the other modes (eg. typ. 95 ns for PicoHarp) Since there is only one photon channel, only autocorrelations can be calculated (unless a router is used). This can be done at the resolution R but of course only starting from lag times larger than the deadtime.	+	[[Dead time]] in T3 Mode is the same as in the other modes (eg. typ. 95 ns for PicoHarp) Since there is only one photon channel, only autocorrelations can be calculated (unless a router is used). This can be done at the resolution R but of course only starting from lag times larger than the [[dead time]].

-	The 32 bit event records are queued in a [[FIFO]] (First In First Out) buffer capable of holding up to 256 k event records. The FIFO input is fast enough to accept records at the full speed of the time-to-digital converters (up to 10 Mcps each). This means, even during a fast burst no events will be dropped except those lost in th dead time anyhow. The FIFO output is continuously read by the host PC, thereby making room for fresh incoming events. Even if the average read rate of the host PC is limited, bursts with much higher rate can be recorded for some time. Only if the average count rate over a long period of time exceeds the readout speed of the PC, a FIFO overrun could occur. In case of a FIFO overrun the measurement must be aborted because data integrity cannot be maintained. However, on a modern and well configured PC with Windows 2000 or XP a sustained average count rate over 4 Mcps is possible. This total transfer rate is fully available for input channel 1. For all practically relevant fluorescence detection applications this is more than sufficient.	+	The 32 bit event records are queued in a [[FIFO]] (First In First Out) buffer capable of holding up to 256 k event records. The FIFO input is fast enough to accept records at the full speed of the time-to-digital converters (up to 10 Mcps each). This means, even during a fast burst no events will be dropped except those lost in the [[dead time]] anyhow. The FIFO output is continuously read by the host PC, thereby making room for fresh incoming events. Even if the average read rate of the host PC is limited, bursts with much higher rate can be recorded for some time. Only if the average count rate over a long period of time exceeds the readout speed of the PC, a FIFO overrun could occur. In case of a FIFO overrun the measurement must be aborted because data integrity cannot be maintained. However, on a modern and well configured PC with Windows 2000 or XP a sustained average count rate over 4 Mcps is possible. This total transfer rate is fully available for input channel 1. For all practically relevant fluorescence detection applications this is more than sufficient.

	For maximum throughput, T3 Mode data streams are normally written directly to disk. The current Harp software does not provide any immediate data visualization during a T3 Mode measurement, except count rate and progress display. However, using custom software it is also possible to analyze incoming data "on the fly". Even on-line correlation can be implemented. Obviously this requires efficient processing and possible restrictions in average count rate. The Harp software installation CD contains demo programs showing how T3 Mode files can be read by custom software. The implementation of custom measurement programs requires the *Harp programming library, which is available as a separate option.		For maximum throughput, T3 Mode data streams are normally written directly to disk. The current Harp software does not provide any immediate data visualization during a T3 Mode measurement, except count rate and progress display. However, using custom software it is also possible to analyze incoming data "on the fly". Even on-line correlation can be implemented. Obviously this requires efficient processing and possible restrictions in average count rate. The Harp software installation CD contains demo programs showing how T3 Mode files can be read by custom software. The implementation of custom measurement programs requires the *Harp programming library, which is available as a separate option.

	see also [[t2-mode]]		see also [[t2-mode]]

bifl

Anonymous (anonymous@undisclosed.example.com) — 2015-02-10T16:34:08+00:00

2013/08/06 14:36		current
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	BIFL stands for Burst Integrated Fluorescence Lifetime: The photon events of a complete burst are accumulated into a [[TCSPC]] histogram which is used for lifetime analysis methods afterwards. Usually a burst is defined as a time interval for which the intensity of a time trace or [[MCS]] measurement is above a chosen threshold. Evaluation of all bursts present in an [[MCS]] trace, for example, results in a lifetime histogram.		BIFL stands for Burst Integrated Fluorescence Lifetime: The photon events of a complete burst are accumulated into a [[TCSPC]] histogram which is used for lifetime analysis methods afterwards. Usually a burst is defined as a time interval for which the intensity of a time trace or [[MCS]] measurement is above a chosen threshold. Evaluation of all bursts present in an [[MCS]] trace, for example, results in a lifetime histogram.

-	BIFL is supported by the [[SymPhoTime]] software, alongside with a variety of burst related techniques.	+	BIFL is supported by the [[software:SymPhoTime]] software, alongside with a variety of burst related techniques.

pile-up_effect

Anonymous (anonymous@undisclosed.example.com) — 2015-06-03T15:09:55+00:00

2015/03/26 12:10		current
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-	{{tag>pile-up TCSPC}}	+	{{tag> TCSPC pile-up dead_time}}
		+	~~TOC~~

	====== Pile-Up Effect ======		====== Pile-Up Effect ======
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	{{ :glossary:pile-up_example.png?600 \|}}		{{ :glossary:pile-up_example.png?600 \|}}
-

mcs

Anonymous (anonymous@undisclosed.example.com) — 2014-01-21T16:39:04+00:00

2013/08/09 07:34		current
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	====== MCS ======		====== MCS ======

-	MCS stands for Multi Channel Scaler. At PQ this term is used in the following context: Single photon events, as originating from a [[TTTR]] measurement are sorted by means of their macroscopic time into equally spaced time bins. What immediately results is a time trace of the fluorescence intensity. In a subsequent analysis the binned ensemble of photons can be used to form [[TCSPC]] histograms, which in turn can be used for lifetime analysis, time-gated analysis etc.	+	MCS stands for Multi Channel Scaler. At PicoQuant this term is used in the following context: Single photon events, as originating from a [[TTTR]] measurement are sorted by means of their macroscopic time into equally spaced time bins. What immediately results is a time trace of the fluorescence intensity. In a subsequent analysis the binned ensemble of photons can be used to form [[TCSPC]] histograms, which in turn can be used for lifetime analysis, time-gated analysis etc.

-	At PQ, MCS is solely supported by our [[SymPhoTime]] package, at the moment.

tcspc

Anonymous (anonymous@undisclosed.example.com) — 2014-01-28T13:06:31+00:00

2013/08/09 15:11		current
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	====== TCSPC ======		====== TCSPC ======

-	TCSPC stands for Time Correlated Single Photon Counting: A stream of photons is recorded, each photon with respect to a (often periodical) signal, e.g. a repeated laser pulse. The single photon events are sorted into histogram channels that correspond to the time that elapsed since the last excitation pulse. It is a time domain method of investigating time resolved fluorescence. [[Products:TimeHarp 260]], [[Products:HydraHarp 400]] and [[Products:PicoHarp 300]] use TCSPC.	+	TCSPC stands for Time Correlated Single Photon Counting: A stream of photons is recorded, each photon with respect to a (often periodical) signal, e.g. a repeated laser pulse. The single photon events are sorted into histogram channels that correspond to the time that elapsed since the last excitation pulse. It is a time domain method for investigating time resolved fluorescence.