Time-Resolved Fluorescence Wiki

pile-up_effect

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

2015/06/03 17:09		current
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-	{{tag>pile-up TCSPC pile-up dead_time}}	+	{{tag> TCSPC pile-up dead_time}}
	~~TOC~~		~~TOC~~

dead_time

Anonymous (anonymous@undisclosed.example.com) — 2015-06-03T15:04:41+00:00

2015/06/03 17:04		current
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	In TCSPC the term dead time refers to the time the TCSPC system needs armed again after detecting an event. During the dead time the TCSPC system is blind.		In TCSPC the term dead time refers to the time the TCSPC system needs armed again after detecting an event. During the dead time the TCSPC system is blind.

-	If for example two photons are detected with the dead time of the TCSPC device the second photon will be lost. This leads to the so called [[glossary:Pile Up Effect]].	+	If for example two photons are detected with the dead time of the TCSPC device the second photon will be lost. This leads to the so called [[glossary:Pile-up Effect]].

	Note that not only TCSPC devices but also photon counting devices exhibit dead times.		Note that not only TCSPC devices but also photon counting devices exhibit dead times.

pre-histogrammed_image

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

2018/01/24 15:40		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 \|

differential_count_rate

Anonymous (anonymous@undisclosed.example.com) — 2017-09-26T11:46:03+00:00

2017/09/24 05:34		current
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	Not really. In case of pulsed signals the average count rate is a misleading quantity. An average count rate value does not take into account when and how those photons are emitted and detected. Interpreting a 100 kcps intensity as a constant emission rate (Poisson mean rate, in math terms) is a misconception. The physics of the measurement is completely different. These photons are obviously not emitted evenly, one by one over the whole one second period. They arrive to the detector bunched, as flashes. These are short time intervals with huge photon density (rate), separated by long "dark", quiet periods.		Not really. In case of pulsed signals the average count rate is a misleading quantity. An average count rate value does not take into account when and how those photons are emitted and detected. Interpreting a 100 kcps intensity as a constant emission rate (Poisson mean rate, in math terms) is a misconception. The physics of the measurement is completely different. These photons are obviously not emitted evenly, one by one over the whole one second period. They arrive to the detector bunched, as flashes. These are short time intervals with huge photon density (rate), separated by long "dark", quiet periods.

-	Getting a final count at "1% of SYNC rate" is a result of **low sampling rate of a high rate signal**.	+	In yet another words, achieving a final count rate at "1% of SYNC rate" is a result of **sparse sampling with dead time**. The sampled signal features much higher photon density, but lasts only for a short time.

	In mathematical terms, "average count rate of 1..2% of SYNC rate" means the overall detection probability, integrated over the whole duration of a measurement. The concept of //differential count rate// is related to the //probability density function//. The detected signal in TCSPC has a very inhomogeneous time distribution.		In mathematical terms, "average count rate of 1..2% of SYNC rate" means the overall detection probability, integrated over the whole duration of a measurement. The concept of //differential count rate// is related to the //probability density function//. The detected signal in TCSPC has a very inhomogeneous time distribution.

	Note: for detectors that exhibit count rate dependent shifting of the IRF, extra care has to be taken when measuring the IRF and directly using it for decay analysis. ((Takuhiro Otosu, Kunihiko Ishii and Tahei Tahara, Note: Simple calibration of the counting-rate dependence of the timing shift of single photon avalanche diodes by photon interval analysis, Rev. Sci. Instrum. 84, 036105 (2013); [[http://dx.doi.org/10.1063/1.4794769]]))		Note: for detectors that exhibit count rate dependent shifting of the IRF, extra care has to be taken when measuring the IRF and directly using it for decay analysis. ((Takuhiro Otosu, Kunihiko Ishii and Tahei Tahara, Note: Simple calibration of the counting-rate dependence of the timing shift of single photon avalanche diodes by photon interval analysis, Rev. Sci. Instrum. 84, 036105 (2013); [[http://dx.doi.org/10.1063/1.4794769]]))

tttr

Anonymous (anonymous@undisclosed.example.com) — 2015-02-10T16:42:50+00:00

2015/02/10 17:42		current
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	The [[Products:TimeHarp 200]] (also the [[Products:TimeHarp 100]]), the [[Products:PicoHarp 300]] [[Products:HydraHarp 400]] support TTTR mode measurements. With the the [[Products:PicoHarp 300]] a slight shift in the nomenclature was introduced. Due to its capability of simultaneously recording both signal inputs (in interactive mode used as 'Start' and 'Stop') as two separate TTTR traces with a time resolution of 4ps, a new TTTR mode was introduced, the so called T2-mode. The traditional recording as with the [[Products:TimeHarp 200]] / [[Products:TimeHarp 100]] is called [[T3-mode]]. In [[T2-mode]] both signal inputs are functionally identical.		The [[Products:TimeHarp 200]] (also the [[Products:TimeHarp 100]]), the [[Products:PicoHarp 300]] [[Products:HydraHarp 400]] support TTTR mode measurements. With the the [[Products:PicoHarp 300]] a slight shift in the nomenclature was introduced. Due to its capability of simultaneously recording both signal inputs (in interactive mode used as 'Start' and 'Stop') as two separate TTTR traces with a time resolution of 4ps, a new TTTR mode was introduced, the so called T2-mode. The traditional recording as with the [[Products:TimeHarp 200]] / [[Products:TimeHarp 100]] is called [[T3-mode]]. In [[T2-mode]] both signal inputs are functionally identical.

-	Today recording of [[glossary:T3-mode]] and T2 mode files is possible with all recent PicoQuant TCSPC devices ([[Products:TimeHarp 260]], [[Products:PicoHarp 300]] and [[Products:HydraHarp 400]] and their included software, analysis is supported mainly by the [[software:SymPhoTime]] software package.	+	Today recording of [[glossary:T3-mode]] and [[glossary:T2-mode]] files is possible with all recent PicoQuant TCSPC devices ([[Products:TimeHarp 260]], [[Products:PicoHarp 300]] and [[Products:HydraHarp 400]] and their included software, analysis is supported mainly by the [[software:SymPhoTime]] software package.

	Due to its capability of including external TTL pulses as markers in the stream of photon events TTTR mode is suitable for [[FLIM]] measurements. The markers are used to synchronise the photon events with a scanning process allowing to sort the photons into image pixels.		Due to its capability of including external TTL pulses as markers in the stream of photon events TTTR mode is suitable for [[FLIM]] measurements. The markers are used to synchronise the photon events with a scanning process allowing to sort the photons into image pixels.

poisson_distribution

Anonymous (anonymous@undisclosed.example.com) — 2014-04-09T20:47:01+00:00

2014/04/09 22:46		current
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	$$P_{\nu}(n)={{\nu^n~e^{-\nu}}\over{n!}}$$		$$P_{\nu}(n)={{\nu^n~e^{-\nu}}\over{n!}}$$

-	The Poisson distribution is of interest especially for [[TCSPC]]: The expected number of photons in any TCSPC channel is given by the 'real' decay (including convolution with the IRF etc.), while the stochastic nature of the measurement process (either a photon is detected or it is not) introduces noise, which follows a Poisson distribution. In the limit of large ${\nu}^{}_{}$ the Poisson distribution approaches a [[Gaussian distribution]] with a width of $\sqrt{\nu}$ centred around ${\nu}^{}_{}$.	+	The Poisson distribution is of interest especially for [[TCSPC]]: The expected number of photons in any TCSPC channel is given by the 'real' decay (including convolution with the IRF etc.), while the stochastic nature of the measurement process (either a photon is detected or it is not) introduces noise, which follows a Poisson distribution. In the limit of large ${\nu}^{}_{}$ the Poisson distribution approaches a [[wp>Normal_distribution\|Gaussian distribution]] with a width of $\sqrt{\nu}$ centred around ${\nu}^{}_{}$.

	In the Gaussian limit [[least squares]] [[wp>Regression_analysis\|fitting]] may be applied, otherwise [[MLE]] [[wp>Regression_analysis\|fitting]] is preferable.		In the Gaussian limit [[least squares]] [[wp>Regression_analysis\|fitting]] may be applied, otherwise [[MLE]] [[wp>Regression_analysis\|fitting]] is preferable.

tcspc

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

2014/01/28 14:06		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.	+	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.

bifl

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

2014/04/09 22:38		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 [[products: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.

fwhm

Anonymous (anonymous@undisclosed.example.com) — 2013-08-06T14:45:49+00:00

2013/08/06 16:45		current
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	FWHM stands for Full Width at Half-Maximum: a measure for the broadness of a peak, for example, of the [[IRF]] in an [[TCSPC]] measurement or the focal width(s) in a [[FLIM]] measurement.		FWHM stands for Full Width at Half-Maximum: a measure for the broadness of a peak, for example, of the [[IRF]] in an [[TCSPC]] measurement or the focal width(s) in a [[FLIM]] measurement.

-	see also [[wp:FWHM]]	+	see also [[wp>FWHM]]

least_squares

Anonymous (anonymous@undisclosed.example.com) — 2014-04-09T20:43:37+00:00

2014/04/09 22:42		current
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	====== Least squares ======		====== Least squares ======

-	Least squares is an optimization paradigm for matching data ('fitting') with a parametrised model equation. A famous example is the linear regression used for finding the linear equation that best matches a given set of data points.	+	Least squares is an optimization paradigm for matching data ('{{wiki>Regression_analysis\|fitting}}') with a parametrised model equation. A famous example is the linear regression used for finding the linear equation that best matches a given set of data points.

	The least squares measure for the goodness-of-fit is		The least squares measure for the goodness-of-fit is

mcs

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

2014/01/21 17:38		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.

residuals

Anonymous (anonymous@undisclosed.example.com) — 2015-02-10T16:35:23+00:00

2014/04/09 22:45		current
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	$$w_i=\sqrt{D_i^{exp}}$$		$$w_i=\sqrt{D_i^{exp}}$$

-	The resudials trace is of importance within any framework concerned with fitting, as the [[products:SymPhoTime]] software or [[products:FluoFit]].	+	The resudials trace is of importance within any framework concerned with fitting, as the [[software:SymPhoTime]] software or [[software:FluoFit]].