Time-Resolved Fluorescence Wiki

fluorescence_correlation_spectroscopy-_a_short_introduction

Anonymous (anonymous@undisclosed.example.com) — 2024-10-11T08:30:57+00:00

2023/02/17 13:43		current
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	{{tag>MicroTime LSM Theory SymPhoTime FCS Correlation}}		{{tag>MicroTime LSM Theory SymPhoTime FCS Correlation}}

-	~~TOC~~	+

	====== Introduction to Fluorescence Correlation Spectroscopy ======		====== Introduction to Fluorescence Correlation Spectroscopy ======

symphotime_tips_and_tricks

Anonymous (anonymous@undisclosed.example.com) — 2020-04-03T14:54:26+00:00

2020/04/03 16:54		current
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-	~~TOC~~

	{{tag>Howto Analysis Tutorial SymPhoTime Tips&Tricks}}		{{tag>Howto Analysis Tutorial SymPhoTime Tips&Tricks}}
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	====== SymPhoTime 64 Analysis Tips and Tricks ======		====== SymPhoTime 64 Analysis Tips and Tricks ======
		+
		+	~~TOC~~
		+
	===== Summary =====		===== Summary =====

start

Anonymous (anonymous@undisclosed.example.com) — 2021-06-17T14:47:30+00:00

2020/05/04 14:11		current
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-	<WRAP center round box 60%>
-	===== News from the community=====
-	* 29.04.20 [[https://www.fret.community/announcement-protein-folding-and-dynamics-webinar/\|Protein folding and dynamics Webinar-Series.]]
-	* 14.04.20 [[https://analyticalscience.wiley.com/do/10.1002/was.00050003/full/bioimagedataanalysis.pdf\|Bioimage Data Analysis.]] New Expanded version of a nice open-source introduction. \\ \\
-	* 14.04.20 [[https://science.sciencemag.org/content/368/6486/78\|De novo design of protein logic gates.]] Exciting fundamental enzymology work. Chen et al. describe the design of logic gates that can regulate protein association. \\ \\
-
-
-
-	[[general:community_news\|...see more...]]
-	</WRAP>

how_to_measure_the_instrument_response_function_irf

Anonymous (anonymous@undisclosed.example.com) — 2023-09-07T22:55:03+00:00

2023/09/08 00:54		current
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	===== Using samples with ultrafast decay =====		===== Using samples with ultrafast decay =====

-	Some detectors (particularly SPADs) have wavelength dependent timing response. In this case an IRF recorded at the excitation wavelength may not be useful for precise reconvolution. The solution is to acquire the IRF at the fluorescence wavelength, or at least spectrally closer to the fluorescence emission.	+	Some detectors (particularly MPD SPADs) have a wavelength dependent timing response. In this case an IRF recorded at the excitation wavelength may not be useful for precise reconvolution. The solution is to acquire the IRF at the fluorescence wavelength, or at least spectrally closer to the fluorescence emission wavelength.

	==== General recipe ====		==== General recipe ====

flim_fcs_using_olympus_fluoview_fv3000_lsm_upgrade_kit

Anonymous (anonymous@undisclosed.example.com) — 2020-05-18T14:01:42+00:00

2020/05/18 16:01		current
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-	{{tag> video FLIM cquisition howto demo Olympus FV3000 LSM_upgrade}}	+	{{tag> video FLIM acquisition howto demo Olympus FV3000 LSM_upgrade}}

flim-fret_measurement_using_an_olympus_fv1200_with_a_flim_and_fcs_upgrade

Anonymous (anonymous@undisclosed.example.com) — 2020-05-18T12:53:40+00:00

2015/02/25 14:54		current
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	The general principles of the data acquisition are analogous in all LSM upgrade kits.		The general principles of the data acquisition are analogous in all LSM upgrade kits.
-	The movie was recorded in 02/2014; the recording procedure may be slightly different in older or newer	+	The movie was recorded in 02/2018; the recording procedure may be slightly different in older or newer
	models.		models.

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	{{topic>howto +IRF &nodate&nouser}}		{{topic>howto +IRF &nodate&nouser}}
	{{topic>howto +FLIM +FRET +analysis &nodate&nouser}}		{{topic>howto +FLIM +FRET +analysis &nodate&nouser}}
-	{{topic>howto +FLIM +Nikon}}

burst_duration_and_fcs_diffusion_time

Anonymous (anonymous@undisclosed.example.com) — 2026-01-12T14:58:02+00:00

2026/01/12 15:56		current
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	Gopich, I. V.; Szabo, A. Journal of Chemical Physics 2005, 122, 014707.		Gopich, I. V.; Szabo, A. Journal of Chemical Physics 2005, 122, 014707.

-	Ruttinger, S. Dissertation, 2006.	+	Ruettinger, S. Dissertation, 2006.

-	Dorr, D. Dissertation, 2014.	+	Doerr, D. Dissertation, 2014.

applications

Anonymous (anonymous@undisclosed.example.com) — 2026-01-12T10:25:53+00:00

2023/02/23 09:12		current
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	[[howto:antibunching_measurements\|Photon antibunching measurements]]		[[howto:antibunching_measurements\|Photon antibunching measurements]]
		+
		+	[[howto:burst_duration_and_fcs_diffusion_time:burst_duration_and_fcs_diffusion_time\|Burst Duration and FCS Diffusion Time]]


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	[[howto:calculate_ratiometric_single_pair_fret_distributions\|Calculate ratiometric single pair FRET distributions]]		[[howto:calculate_ratiometric_single_pair_fret_distributions\|Calculate ratiometric single pair FRET distributions]]
		+
		+	[[howto:burst_duration_and_fcs_diffusion_time:burst_duration_and_fcs_diffusion_time\|Burst Duration and FCS Diffusion Time]]

basics

Anonymous (anonymous@undisclosed.example.com) — 2024-10-11T08:23:47+00:00

2021/09/23 14:59		current
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	{{tag> basics introduction FCS fluorescence microscopy objective resolution NA tutorials}}		{{tag> basics introduction FCS fluorescence microscopy objective resolution NA tutorials}}
-	===== Basics =====	+	====== Basics ======

	* [[video_tutorials\|Fluorescence and Fluorescence Microscopy by Nico Stuurman]]		* [[video_tutorials\|Fluorescence and Fluorescence Microscopy by Nico Stuurman]]

imprint

Anonymous (anonymous@undisclosed.example.com) — 2018-05-23T08:30:11+00:00

2018/05/23 10:29		current
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	https://www.picoquant.com\\		https://www.picoquant.com\\

-	Vertretungsberechtiger Geschäftsführer/General Manager: Rainer Erdmann	+	Vertretungsberechtiger Geschäftsführer/General Manager: Rainer Erdmann\\
-	HRB 60901 Berlin-Charlottenburg	+	HRB 60901 Berlin-Charlottenburg\\
-	VAT ID: DE 812140373	+	VAT ID: DE 812140373\\
-	WEEE-Reg.-Nr. DE 96457402	+	WEEE-Reg.-Nr. DE 96457402\\
-	Tax-ID.: 37/098/45817	+	Tax-ID.: 37/098/45817\\

lsm710

Anonymous (anonymous@undisclosed.example.com) — 2016-07-21T13:31:38+00:00

2016/07/20 14:05		current
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-	====== FLIM Measurement Using a Zeiss LSM710 with a FLIM and FCS Upgrade ======	+	====== FLIM Measurement Using a Zeiss LSM710/LSM780/LSM880 with a FLIM and FCS Upgrade ======

	This tutorial shows the recording of FLIM images using an LSM upgrade kit, in this case a Zeiss LSM710.		This tutorial shows the recording of FLIM images using an LSM upgrade kit, in this case a Zeiss LSM710.
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	* to monitor concentration changes using a reporter dye		* to monitor concentration changes using a reporter dye

-	* To monitor interactions between two molecules via FRET.	+	* To monitor interactions between two molecules via FRET. \\
		+
		+
		+	\\
		+	{{ youtube>QXGqA2IsivM?large }} \\

	The data acquisition is analogous also for upgrades on an LSM780 or LSM880, and the general principles of the data acquisition are analogous in all LSM upgrade kits.		The data acquisition is analogous also for upgrades on an LSM780 or LSM880, and the general principles of the data acquisition are analogous in all LSM upgrade kits.
		+	\\ \\
		+	\\
		+	{{ youtube>vofLPLVmq-Q?large }} \\

-	{{ youtube>QXGqA2IsivM?large }}

measurement_hardware_instrumentation

Anonymous (anonymous@undisclosed.example.com) — 2018-06-25T07:18:07+00:00

2018/06/25 09:17		current
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	[[video_tutorials#Kurt Thorn: Optical Sectioning and Confocal Microscopy\|Confocal microscoy and optical sectioning by Kurt Thorn]]		[[video_tutorials#Kurt Thorn: Optical Sectioning and Confocal Microscopy\|Confocal microscoy and optical sectioning by Kurt Thorn]]

-	[[technical docs:Beampath of the Zeiss LSM880]]	+	[[Beampath of the Zeiss LSM880]]

	[[howto:check_overlap_of_different_color_confocal_volumes\|How to check the overlap of different color confocal volumes]]		[[howto:check_overlap_of_different_color_confocal_volumes\|How to check the overlap of different color confocal volumes]]

software

Anonymous (anonymous@undisclosed.example.com) — 2025-05-28T07:47:47+00:00

2025/05/28 09:18		current
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	{{tag> software acquisition analysis}}		{{tag> software acquisition analysis}}

-	~~TOC~~

	====== Software ======		====== Software ======

supported_th260_pc

Anonymous (anonymous@undisclosed.example.com) — 2017-09-20T15:42:57+00:00

2017/07/24 10:03		current
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		+	/*
	{{tag> PC TH260 Harps TCSPC}}		{{tag> PC TH260 Harps TCSPC}}
	~~TOC~~		~~TOC~~
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	\|HP ENVY 700-056 \|AMD A75 FCH\| \|		\|HP ENVY 700-056 \|AMD A75 FCH\| \|
	\|Dell Precision T3400 \|Intel X38 \| Installed in SLOT 3 , PCIe 8x(4,1)\|		\|Dell Precision T3400 \|Intel X38 \| Installed in SLOT 3 , PCIe 8x(4,1)\|
		+	\|Dell Optiplex 990 \|Intel X38 \| PCIe 8x \| /* See ticket 828080*\

	===== not-working mainboards / computer =====		===== not-working mainboards / computer =====
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	\|HP 200-G1 (Model L5L54US#ABA) \| \| \|		\|HP 200-G1 (Model L5L54US#ABA) \| \| \|
	\|Lenovo ThinkServer TS140 \| \| \|		\|Lenovo ThinkServer TS140 \| \| \|
		+
		+	*/

start

Anonymous (anonymous@undisclosed.example.com) — 2025-02-14T09:43:52+00:00

2025/02/14 10:43		current
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	In this article we assume that both detectors are SPADs of the same kind (both Excelitas SPADs, or both PDM-SPADs, or both tau-SPADs).		In this article we assume that both detectors are SPADs of the same kind (both Excelitas SPADs, or both PDM-SPADs, or both tau-SPADs).

-	If you are using either a proper (see below) 50/50 cube beamsplitter to split the signal between two detectors or a 100% mirror to direct the signal to one detector and then the other, but still observe very different count rates on the two detectors, this discrepancy could be due to the following reasons:	+	If you are using either a proper (see below) 50/50 beamsplitter to split the signal between two detectors or a 100% mirror to direct the signal to one detector and then the other, but still observe very different count rates on the two detectors, this discrepancy could be due to the following reasons:

	1. Misalignment of the Lens in Front of the SPAD:		1. Misalignment of the Lens in Front of the SPAD:

advantages_and_disadvantages_of_two_photon_excitation_tpe

Anonymous (anonymous@undisclosed.example.com) — 2014-01-28T13:07:58+00:00

2014/01/28 14:07		current
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-	{{tag>TPE}}
	====== Advantages and disadvantages of two photon excitation (TPE) ======		====== Advantages and disadvantages of two photon excitation (TPE) ======

fcs

Anonymous (anonymous@undisclosed.example.com) — 2015-01-22T14:55:15+00:00

2015/01/22 15:54		current
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	====== Fluorescence Correlation Spectroscopy (FCS) ======		====== Fluorescence Correlation Spectroscopy (FCS) ======
		+	Fluorescence correlation spectroscopy (FCS) is a correlation analysis of fluctuation of the fluorescence intensity. The analysis provides parameters of the physics under the fluctuations. One of the interesting applications of this is an analysis of the concentration fluctuations of fluorescent particles (molecules) in solution. In this application, the fluorescence emitted from a very tiny space in solution containing a small number of fluorescent particles (molecules) is observed. The fluorescence intensity is fluctuating due to Brownian motion of the particles. In other words, the number of the particles in the sub-space defined by the optical system is randomly changing around the average number. The analysis gives the average number of fluorescent particles and average diffusion time, when the particle is passing through the space. Eventually, both the concentration and size of the particle (molecule) are determined. Both parameters are important in biochemical research, biophysics, and chemistry.(([[http://en.wikipedia.org/wiki/Fluorescence_correlation_spectroscopy]]))
		+

	see [[general:fluorescence_correlation_spectroscopy-_a_short_introduction\|Introduction to Fluorescence Correlation Spectroscopy]].		see [[general:fluorescence_correlation_spectroscopy-_a_short_introduction\|Introduction to Fluorescence Correlation Spectroscopy]].

support_plane_analysis

Anonymous (anonymous@undisclosed.example.com) — 2014-01-21T16:46:58+00:00

2014/01/21 17:46		current
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	===== References =====		===== References =====

-	Lakowicz JR (1999)// Principles of Fluorescence Spectroscopy//, 2nd edn. Kluver Academic/Plenum Publishers, New York (available in room C202)*	+	*Lakowicz JR (1999)// Principles of Fluorescence Spectroscopy//, 2nd edn. Kluver Academic/Plenum Publishers, New York

data_file_import

Anonymous (anonymous@undisclosed.example.com) — 2022-08-04T13:24:27+00:00

2022/08/04 14:53		current
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	\\		\\
	After expanding the data container:		After expanding the data container:
-	{{ :howto:et2_workspace2.png?340 \|}}	+	{{ :howto:et2_workspace2.png \|}}

	Two histograms have been imported. They are shown as "Decay" because EasyTau does not know their assignment yet.		Two histograms have been imported. They are shown as "Decay" because EasyTau does not know their assignment yet.
		+	\\
		+	\\
		+
		+
		+	==== Multiple File Import ====
		+
		+	Importing multiple data files is easy. Use CTRL + Click to select multiple files:
		+
		+	{{ :howto:et2_fileimport2.png \|}}
		+	\\
		+	\\
		+	Each input ''.phu'' file has got a dedicated ''.etc'' data container:
		+	{{ :howto:et2_workspace3.png \|}}
		+	\\
		+	\\
		+	Unlike ''Decay_Coumarin_6.phu'' containing two histograms, both ''Anthracene_EtOH.phu'' and ''IRF375.phu'' contains only one histogram. These two measurements actually belong to each other. In order to perform reconvolution fitting of the Antracene decay, the corresponding IRF measured at 375nm excitation wavelength will be needed.
		+

flim_measurement_using_a_nikon_a1_with_a_flim_and_fcs_upgrade

Anonymous (anonymous@undisclosed.example.com) — 2015-06-30T13:07:15+00:00

2015/06/16 13:47		current
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	The general principles of the data acquisition are analogous in all LSM upgrade kits.		The general principles of the data acquisition are analogous in all LSM upgrade kits.
-	The movie was recorded in 02/2014; the recording procedure may be somewhat different in older or newer	+	The movie was recorded in 02/2014 and shows the integration with Nikon A1 system with a NIS version lower than 4.3; the recording procedure may be somewhat different in higher or very old versions.
-	models.	+

	{{ youtube>1Tr9DZ-SkSQ?large }}		{{ youtube>1Tr9DZ-SkSQ?large }}

how_to_work_with_the_instrument_response_function_irf

Anonymous (anonymous@undisclosed.example.com) — 2023-02-17T12:41:49+00:00

2021/03/23 11:49		current
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-	{{tag>howto IRF tutorial analysis MT LSM_upgrade}}	+	{{tag>howto IRF tutorial analysis MicroTime LSM_upgrade}}

pattern_matching

Anonymous (anonymous@undisclosed.example.com) — 2014-06-18T13:26:07+00:00

2014/05/23 09:39		current
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	Pattern Matching Analysis by decomposing a recorded image into different user-defined patterns. Display of the calculated data using an RGB false color model. The calculated amplitudes of the first three defined patterns are depicted in three different colors for each pixel.		Pattern Matching Analysis by decomposing a recorded image into different user-defined patterns. Display of the calculated data using an RGB false color model. The calculated amplitudes of the first three defined patterns are depicted in three different colors for each pixel.
		+
		+	{{ youtube>L68IgRbNSLE?large }}

	==== Open an Image ====		==== Open an Image ====

start

Anonymous (anonymous@undisclosed.example.com) — 2026-02-11T14:19:03+00:00

2024/12/19 16:57		current
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	{{topic>howto -FT300 -sample -analysis -draft &nodate&nouser}}		{{topic>howto -FT300 -sample -analysis -draft &nodate&nouser}}

-	===== NovaFLIM / Analysis =====
-
-	{{topic>howto +tutorial +novaflim -draft &nodate&nouser}}

	===== SymPhoTime64 / Analysis =====		===== SymPhoTime64 / Analysis =====

update

Anonymous (anonymous@undisclosed.example.com) — 2023-02-23T06:37:29+00:00

2023/02/23 07:24		current
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	===== Introduction =====		===== Introduction =====
	This tutorial shows step-by-step, how the FLIM script of SymPhoTime 64 can be used to fit several regions of interest (ROIs), and how to extract and interpret the results. In detail, the FLIM script is started using an image of mouse kidney tissue in the “Tutorials” workspace, [[https://figshare.com/s/4957fcfa684daef86c23]], a suited fitting model is chosen and a pixel-by-pixel fit is performed.\\		This tutorial shows step-by-step, how the FLIM script of SymPhoTime 64 can be used to fit several regions of interest (ROIs), and how to extract and interpret the results. In detail, the FLIM script is started using an image of mouse kidney tissue in the “Tutorials” workspace, [[https://figshare.com/s/4957fcfa684daef86c23]], a suited fitting model is chosen and a pixel-by-pixel fit is performed.\\
		+
		+
		+	===== Step-by-step Tutorial =====
		+
		+	==== Select a file and start the analysis ====
		+
		+	* Start SymPhoTime 64 software (this tutorial uses version 2.5, there might be differences when working with other versions).
		+	* Open the “Tutorials” workspace via File -> Open Workspace from the main menu.\\
		+
		+	Response:\\
		+	The files of the sample workspace are displayed in the workspace panel on the left side of the main window.
		+	* Highlight the file ''Kidney_Cells_FLIM.ptu'' by a single mouse click.
		+	* Select the "Analysis" tab and in there, open the "Imaging" drop-down menu.\\
		+	* Start the FLIM script by clicking on "Start".\\
		+
		+	{{ howto:startflim.png?200 \|}}
		+
		+
		+	Response:\\
		+	The FLIM analysis is applied to the file ''Kidney_Cells_FLIM.ptu''. Thereby, a new Window opens:
		+
		+	{{ howto:kidneyfullscreen3.png \|}}
		+
		+
		+	Note:\\
		+	The window contains five different sections:\\
		+	1: Setting panel\\
		+	Imaging analysis options can be defined in this section.\\
		+	2: [[glossary:Fast FLIM]] image\\
		+	The FLIM preview image displayed in a false color scale. The brightness encodes the intensity, while the color encodes the average "Fast FLIM" lifetime, i.e. the mean arrival times of the photons after the laser pulse. When not defined otherwise, intensity and color scale stretch from minimum to maximum. As the mean arrival time of the background photons in the areas where no fluorescence is detected, is randomly spread over the TCSPC window, the mean photon arrival time of the dark background is usually very long (with an average up to 1/2 of the TCSPC window), which makes the color scale loaded by default sometimes unsuited for displaying the lifetime contrast in the actual sample. In this case, the scale can be adapted.\\
		+	3: Fluorescence Lifetime Histogram\\
		+	Here the frequency of photon counts corresponding to the individual mean lifetimes is plotted. The settings of the plot can be adapted using the controls on the right of the plot. The histogram is photon weighted.\\
		+	4: Decay Fitting Parameters\\
		+	Here the lifetime fitting model can be selected. Fitting is then applied to the lifetime graph(s) on the lower center ([[glossary:TCSPC]] histogram).\\
		+	5: [[glossary:TCSPC]] Decay window\\
		+	By default, this set shows the [[glossary:TCSPC]] histogram of all photons in the image in green (= dataset 0) and the [[glossary:TCSPC]] histogram of a single pixel in grey (= dataset 1). In red an estimation of the instrument response function (=IRF) is shown. The IRF reconstruction is deducted from the rising edge of the [[glossary:TCSPC]] histogram.\\
		+
		+
		+	* To enhance the lifetime contrast, adapt the color scale by typing the limit values for the "Fast Lifetime [ns]" and "Events[cnts]". Additionally set the "Lifetime Histogram" range on the right hand.
		+	* Tick the checkbox of the detection "Data Channel" (i.e. detector), you want to use - in this case detector channel 4 - and press "Calculate FastFLIM".\\
		+
		+	{{ howto:detectionchannel.png?400 \|}}
		+
		+	Response:\\
		+	The FLIM Preview image will get updated. Optimize contrast by adapting "Min" and "Max" values.
		+
		+	==== Select a file and start the analysis ====
		+
		+	* In the FLIM preview image, ROIs can be selected using the context menu (Right Click).\\
		+
		+	{{ howto:selectmagicwand_w.png?300 \|}}
		+
		+	Note:\\
		+
		+	- The following ROI-selection tools are available: Rectangle ROI, Ellipse ROI for simple drawing and Paint ROI for marking the pixels the mouse passed over. The faster the mouse pointer moves, the broader the marked lines will get. Free ROI draws a free shape. The pixels within the drawn shape will be selected. Finally Magic Wand marks area with similar fast lifetime.
		+	- Using keyboard shortcuts ''<CTRL>+<Z>'' you can undo a selection. Redo also with ''<CTRL>+<Shift>+<Z>'' is possible.\\
		+	- You can add several areas to an existing ROI with the same or different selection tool by keeping the ''<Shift>'' key pressed while drawing the additional regions.\\
		+	- If you want to remove some of the pixels from the selected ROI, just keep the ''<CTRL>'' key pressed when using a ROI selection tool to exclude the unwanted parts.\\
		+	- Additionally you can zoom, move or Invert the ROI. Please see the shortcuts provided for each option in the context menu.\\
		+	- If you want to start again from scratch select "Select all as ROI".\\
		+
		+	* In this step, as an example, we mark an ROI with similar lifetime range using the "Magic Wand" tool. The sensitivity of the tool to lifetime differences can be adjusted in a box below the intensity and color scale options.\\
		+
		+	{{ howto:magicwand_w_thresh.png?300 \|}}
		+
		+	* Increase the threshold to 25.\\
		+
		+	{{ howto:inner_magicwand25_3.png \|}}
		+
		+	Response:\\
		+	The parts of the image with a similar fast lifetime range will be selected and the lifetime histogram will get updated accordingly. If you want to combine several spatially separated regions with a similar lifetime into one single ROI, as it's done here, you have to press "Shift" when selecting the spatial separated areas with the Magic wand tool.
		+
		+	Note:\\
		+	Since this function is based on the displayed image, the sensitivity of the selection is dependent on the scaling of the color-encoded component. Changing the color scale (in general the lifetime) can change the sensitivity of this tool.\\
		+
		+
		+	Response:\\
		+	An extra gray decay corresponding to ''ROI 0'' will appear under decay fit in "Decay Fitting" panel.\\
		+
		+
		+	Note:\\
		+	For fine adjustment, you can use any other ROI selection tools from context menu. In this case better to use ''<CTRL>'' or ''<Shift>'' buttons in order to remove pixel with a different or add pixels with similar fast lifetime. Ideally try to select an ROI with 10000 to 100000 counts in peak for getting the optimum statistics. ROIs with lower intensities can also be fitted, but in case of a more-exponential decay, some components might not be resolved.\\
		+
		+
		+	* In order to select an additional ROI, click "New" ROI.\\
		+
		+	{{ howto:addroi.png?400 \|}}
		+
		+
		+	Response:\\
		+	The software assigns sequential numbers to selected ROIs.The whole preview image will appear again.\\
		+
		+	* For the next ROI, first we use the same tool, "Magic Wand" but adapt its threshold to 20.
		+	{{ howto:tubul_magicwand20_3.png \|}}
		+
		+	* Repeat the last two steps in order to select the cell nuclei as the last ROI.\\
		+
		+	{{ howto:nuclei_magicwand30_3.png \|}}
		+
		+	Response:\\
		+	Now you can see fast FLIM (preview) images of "ROI 0", "ROI 1" and "ROI 2" when selecting them in the ROI-list In the Region of Interest-Menu, as well as their corresponding decays in TSCPC window in grey when selecting the different decays in the list.
		+
		+
		+	==== Perform an Initial Lifetime Fit on the Selected Regions (ROIs) ====
		+
		+
		+	* In the forth box, "Decay Fitting", from the Fitting Model drop-down list select "n-Exponential Reconvolution Fit".\\
		+
		+	{{ howto:nexpon_fitmodel.png?400 \|}}
		+
		+	Response:\\
		+	In the TCSPC window, the IRF is displayed in bright red, the data fitting limits are moved to the border of the TCSPC window.\\
		+	The new fitting parameters "Shift IRF" and "Bkgr IRF" (=background IRF) appear in the fitting parameter table.\\
		+
		+	Note:\\
		+	The software offers the possibility to fit the data using an n-exponential tailfit, n-exponential reconvolution or rapid reconvolution fit. A tailfit can be used when the fitted lifetimes are significantly longer than the instrument response function. A reconvolution fit is usually preferable, because the complete decay is fitted, while for a tailfit, the start of the fitting range is usually a bit arbitrary. A rapid reconvolution fit is suited, if the image was measured with a very high countrate and a system with a dead time significantly above the pile-up-limit or when the image has been acquired with a repetition rate, which is normally too high for the lifetime of the dye, so that the decay is not at the background level at the end of the decay window. The rapidFLIM-fitting is explained in another tutorial.\\
		+
		+	For explanation about the fitting model and the used equations, click on the "Help" button next to the selected model. This opens a help window containing the fitting equation and the explanation of the different parameters.\\
		+
		+
		+	* From "Decay" drop-down list select ''ROI 0'' and click "Initial Fit" (marked in orange).\\
		+	{{ howto:inner_monoexpo_3.png \|}}
		+
		+	Response:\\
		+	A single exponential reconvolution fit is performed. In the TCSPC window, the fit is displayed as a black line. Below, the residuals (= difference between raw data and fit values) are displayed.\\
		+	* Fit values appear in the fitting table. Check the fitting curve, residuals and χ².\\
		+
		+	Note:\\
		+	Usually, a decent fit is characterized by the following criteria:\\
		+	The fitted curve overlays well with the decay curve. In the residual window, the values spread randomly around 0.\\
		+	The χ²-value approaches 1.\\
		+	The calculated fitting values are reasonable.\\
		+	The fitting model with least parameters is preferred.\\
		+
		+
		+	* In this example it is obvious that the applied single exponential reconvolution fit is not suited to fit the decay curve. Increase the "Model Parameters" to n = 2. Again, click on "Initial fit".\\
		+
		+	{{ howto:inner_biexpo_3.png \|}}
		+
		+
		+	Response:\\
		+	The fit quality increases. But if it still doesn't look sufficient. One sees a trend in residuals and not a random distribution around 0. Increase number of "Model Parameters" to three.\\
		+
		+	{{ howto:inner_3expo_3.png \|}}
		+
		+	* Here the fitting model shows a satisfying result. A 3-exponential fitting model should be used for ROI 0.\\
		+
		+	* Try the last two steps with "ROI 1".\\
		+
		+	{{ howto:tubul_3expo_3.png \|}}
		+
		+
		+	* Find the best fit for "ROI 2" in a same manner. It is better always to start from monoexponential and try to find the fitting model with a lower number of components.\\
		+	{{ howto:nuclei_3expo_3.png \|}}
		+
		+	* Three components exponential decay seems to be suitable for all three ROIs. If all ROIs can be fitted with the same model, you can also click on "Fit All" to get all curves fitted with the same model.\\
		+	* Clicking on "Fit All" will fit all active data sets with the same model, using the start parameters of the active data set. If you do not want to fit the complete decay (dataset 1) and the decay of a single pixel (Dataset 2), press "Show All" button:
		+
		+
		+	{{ howto:showall.png \|}}
		+
		+	* Uncheck the first two datasets on top of the parameter table and press "Fit All" again.
		+
		+	{{ howto:deselectdataset1_3.png \|}}
		+
		+
		+
		+
		+	==== Compare the lifetimes and save results ====
		+
		+
		+
		+
		+	* In order to compare the lifetime of these three compartments, apart from fitting parameter table shown above, you can plot them by selecting the "Parameter Plot" on the right side of TCSPC window.\\
		+
		+	Note:\\
		+	The X-Axes is showing the "Dataset Number" corresponding to the dataset listed in Decay drop-down menu (in Dcay Fitting Panel). This means by default "Overall Decay" and "Pixel (0,0)", and then selected ROIs.\\
		+	For the Y-Axes one can select one or multiple fit parameters.\\
		+
		+	* Tick the "tau_Av_Int" checkbox for Y-Axes and zoom in to be able to see the lifetime differences better.\\
		+	{{ howto:parameterplot_3rois_3.png \|}}
		+
		+
		+
		+	* At the end, click on "Save Result" button in parameter panel.\\
		+
		+
		+	{{ howto:saveresultbutton.png?300 \|}}
		+
		+
		+	Response:\\
		+	A result file "FLIM.pqres" is stored under the raw data file ''Kidney_Cell_FLIM.ptu''.\\
		+
		+	* Later, clicking on the result file reopens the file in the same way as it was stored.

pycorrfit

Anonymous (anonymous@undisclosed.example.com) — 2016-03-07T11:00:06+00:00

2015/11/03 14:59		current
Line 4:		Line 4:
	"[...] PyCorrFit is a general-purpose FCS evaluation software that, amongst other formats, supports the established Zeiss ConfoCor3 ~.fcs file format. PyCorrFit comes with several built-in model functions, covering a wide range of applications in standard confocal FCS. In addition, it contains equations dealing with different excitation geometries like total internal reflection (TIR)."		"[...] PyCorrFit is a general-purpose FCS evaluation software that, amongst other formats, supports the established Zeiss ConfoCor3 ~.fcs file format. PyCorrFit comes with several built-in model functions, covering a wide range of applications in standard confocal FCS. In addition, it contains equations dealing with different excitation geometries like total internal reflection (TIR)."

-	[[http://paulmueller.github.io/PyCorrFit/]]	+	[[http://pycorrfit.craban.de/]]

	GitHub:[[https://github.com/paulmueller/PyCorrFit]]		GitHub:[[https://github.com/paulmueller/PyCorrFit]]

symphotime64

Anonymous (anonymous@undisclosed.example.com) — 2015-01-22T14:39:59+00:00

2014/05/23 09:34		current
Line 5:		Line 5:


-	The [[http://www.picoquant.com\|PicoQuant]] SymPhoTime 64 software package is an integrated solution for data acquisition and analysis using PicoQuant's time-resolved confocal microscope MicroTime 200, LSM upgrade kits or [[glossary:TCSPC]] electronics. Its clearly structured layout and powerful analysis routines allows the user to focus on the results rather than on the data processing. The software is designed for a 64 bit operation system and features a graphical user interface (GUI), which guides the user through all necessary steps for an individual analysis or measurement process. Data dependencies are directly visible in the underlying workspace concept. An integrated scripting language ("STUPSLANG") even puts the user in a position to freely add new analysis procedures or customize existing ones.	+	The [[http://www.picoquant.com\|PicoQuant]] SymPhoTime 64 software package is an integrated solution for data acquisition and analysis using PicoQuant's time-resolved confocal microscope [[products:MicroTime]], LSM upgrade kits or [[glossary:TCSPC]] electronics. Its clearly structured layout and powerful analysis routines allows the user to focus on the results rather than on the data processing. The software is designed for a 64 bit operation system and features a graphical user interface (GUI), which guides the user through all necessary steps for an individual analysis or measurement process. Data dependencies are directly visible in the underlying workspace concept. An integrated scripting language ("STUPSLANG") even puts the user in a position to freely add new analysis procedures or customize existing ones.

	For more information, latest version and download link see [[http://www.picoquant.com/products/category/software/symphotime-64-fluorescence-lifetime-imaging-and-correlation-software\|SymPhoTime64]].		For more information, latest version and download link see [[http://www.picoquant.com/products/category/software/symphotime-64-fluorescence-lifetime-imaging-and-correlation-software\|SymPhoTime64]].

tcspc_external_markers

Anonymous (anonymous@undisclosed.example.com) — 2020-09-14T16:01:28+00:00

2020/09/14 18:01		current
Line 31:		Line 31:
	* PI Controller: E725		* PI Controller: E725
	* PI Controller: E710 \\		* PI Controller: E710 \\
-	* Controller: E727 \\	+	* PI Controller: E727 \\
	* Controller: C867.2U2 (PI wide range scanner)		* Controller: C867.2U2 (PI wide range scanner)
	* Controller: C867.262 (PI wide range scanner)		* Controller: C867.262 (PI wide range scanner)

dokuwiki

Anonymous (anonymous@undisclosed.example.com) — 2026-04-23T08:17:27+00:00

2026/05/02 16:29	current
Line 1:	Line 1:
	+	====== DokuWiki ======
	+
	+	[[doku>wiki:dokuwiki\|{{wiki:dokuwiki-128.png }}]] DokuWiki is a simple to use and highly versatile Open Source [[wp>wiki]] software that doesn't require a database. It is loved by users for its clean and readable [[wiki:syntax]]. The ease of maintenance, backup and integration makes it an administrator's favorite. Built in [[doku>acl\|access controls]] and [[doku>auth\|authentication connectors]] make DokuWiki especially useful in the enterprise context and the large number of [[doku>plugins]] contributed by its vibrant community allow for a broad range of use cases beyond a traditional wiki.
	+
	+	Read the [[doku>manual\|DokuWiki Manual]] to unleash the full power of DokuWiki.
	+
	+	===== Download =====
	+
	+	DokuWiki is available at https://download.dokuwiki.org/
	+
	+
	+	===== Read More =====
	+
	+	All documentation and additional information besides the [[syntax\|syntax description]] is maintained in the DokuWiki at [[doku>\|www.dokuwiki.org]].
	+
	+	About DokuWiki
	+
	+	* [[doku>features\|A feature list]] :!:
	+	* [[doku>users\|Happy Users]]
	+	* [[doku>press\|Who wrote about it]]
	+	* [[doku>blogroll\|What Bloggers think]]
	+	* [[https://www.wikimatrix.org/show/DokuWiki\|Compare it with other wiki software]]
	+
	+	Installing DokuWiki
	+
	+	* [[doku>requirements\|System Requirements]]
	+	* [[https://download.dokuwiki.org/\|Download DokuWiki]] :!:
	+	* [[doku>changes\|Change Log]]
	+	* [[doku>Install\|How to install or upgrade]] :!:
	+	* [[doku>config\|Configuration]]
	+
	+	Using DokuWiki
	+
	+	* [[doku>syntax\|Wiki Syntax]]
	+	* [[doku>manual\|The manual]] :!:
	+	* [[doku>FAQ\|Frequently Asked Questions (FAQ)]]
	+	* [[doku>glossary\|Glossary]]
	+
	+	Customizing DokuWiki
	+
	+	* [[doku>tips\|Tips and Tricks]]
	+	* [[doku>Template\|How to create and use templates]]
	+	* [[doku>plugins\|Installing plugins]]
	+	* [[doku>development\|Development Resources]]
	+
	+	DokuWiki Feedback and Community
	+
	+	* [[doku>newsletter\|Subscribe to the newsletter]] :!:
	+	* [[doku>mailinglist\|Join the mailing list]]
	+	* [[https://forum.dokuwiki.org\|Check out the user forum]]
	+	* [[doku>irc\|Talk to other users in the IRC channel]]
	+	* [[https://github.com/splitbrain/dokuwiki/issues\|Submit bugs and feature wishes]]
	+	* [[doku>thanks\|Some humble thanks]]
	+
	+
	+	===== Copyright =====
	+
	+	2004-2020 (c) Andreas Gohr <andi@splitbrain.org>((Please do not contact me for help and support -- use the [[doku>mailinglist]] or [[https://forum.dokuwiki.org\|forum]] instead)) and the DokuWiki Community
	+
	+	The DokuWiki engine is licensed under [[https://www.gnu.org/licenses/gpl.html\|GNU General Public License]] Version 2. If you use DokuWiki in your company, consider [[doku>donate\|donating]] a few bucks ;-).
	+
	+	Not sure what this means? See the [[doku>faq:license\|FAQ on the Licenses]].

syntax

Anonymous (anonymous@undisclosed.example.com) — 2026-04-23T08:17:27+00:00

2026/05/02 16:29	current
Line 1:	Line 1:
	+	====== Formatting Syntax ======
	+
	+	[[doku>DokuWiki]] supports some simple markup language, which tries to make the datafiles to be as readable as possible. This page contains all possible syntax you may use when editing the pages. Simply have a look at the source of this page by pressing "Edit this page". If you want to try something, just use the [[playground:playground\|playground]] page. The simpler markup is easily accessible via [[doku>toolbar\|quickbuttons]], too.
	+
	+	===== Basic Text Formatting =====
	+
	+	DokuWiki supports bold, //italic//, __underlined__ and ''monospaced'' texts. Of course you can __//''combine''//__ all these.
	+
	+	DokuWiki supports bold, //italic//, __underlined__ and ''monospaced'' texts.
	+	Of course you can __//''combine''//__ all these.
	+
	+	You can use <sub>subscript</sub> and <sup>superscript</sup>, too.
	+
	+	You can use <sub>subscript</sub> and <sup>superscript</sup>, too.
	+
	+	You can mark something as <del>deleted</del> as well.
	+
	+	You can mark something as <del>deleted</del> as well.
	+
	+	Paragraphs are created from blank lines. If you want to force a newline without a paragraph, you can use two backslashes followed by a whitespace or the end of line.
	+
	+	This is some text with some linebreaks\\ Note that the
	+	two backslashes are only recognized at the end of a line\\
	+	or followed by\\ a whitespace \\this happens without it.
	+
	+	This is some text with some linebreaks\\ Note that the
	+	two backslashes are only recognized at the end of a line\\
	+	or followed by\\ a whitespace \\this happens without it.
	+
	+	You should use forced newlines only if really needed.
	+
	+	===== Links =====
	+
	+	DokuWiki supports multiple ways of creating links.
	+
	+	==== External ====
	+
	+	External links are recognized automagically: http://www.google.com or simply www.google.com - You can set the link text as well: [[http://www.google.com\|This Link points to google]]. Email addresses like this one: <andi@splitbrain.org> are recognized, too.
	+
	+	DokuWiki supports multiple ways of creating links. External links are recognized
	+	automagically: http://www.google.com or simply www.google.com - You can set
	+	link text as well: [[http://www.google.com\|This Link points to google]]. Email
	+	addresses like this one: <andi@splitbrain.org> are recognized, too.
	+
	+	==== Internal ====
	+
	+	Internal links are created by using square brackets. You can either just give a [[pagename]] or use an additional [[pagename\|link text]].
	+
	+	Internal links are created by using square brackets. You can either just give
	+	a [[pagename]] or use an additional [[pagename\|link text]].
	+
	+	[[doku>pagename\|Wiki pagenames]] are converted to lowercase automatically, special characters are not allowed.
	+
	+	You can use [[some:namespaces]] by using a colon in the pagename.
	+
	+	You can use [[some:namespaces]] by using a colon in the pagename.
	+
	+	For details about namespaces see [[doku>namespaces]].
	+
	+	Linking to a specific section is possible, too. Just add the section name behind a hash character as known from HTML. This links to [[syntax#internal\|this Section]].
	+
	+	This links to [[syntax#internal\|this Section]].
	+
	+	Notes:
	+
	+	* Links to [[syntax\|existing pages]] are shown in a different style from [[nonexisting]] ones.
	+	* DokuWiki does not use [[wp>CamelCase]] to automatically create links by default, but this behavior can be enabled in the [[doku>config]] file. Hint: If DokuWiki is a link, then it's enabled.
	+	* When a section's heading is changed, its bookmark changes, too. So don't rely on section linking too much.
	+
	+	==== Interwiki ====
	+
	+	DokuWiki supports [[doku>Interwiki]] links. These are quick links to other Wikis. For example this is a link to Wikipedia's page about Wikis: [[wp>Wiki]].
	+
	+	DokuWiki supports [[doku>Interwiki]] links. These are quick links to other Wikis.
	+	For example this is a link to Wikipedia's page about Wikis: [[wp>Wiki]].
	+
	+	==== Windows Shares ====
	+
	+	Windows shares like [[\\server\share\|this]] are recognized, too. Please note that these only make sense in a homogeneous user group like a corporate [[wp>Intranet]].
	+
	+	Windows Shares like [[\\server\share\|this]] are recognized, too.
	+
	+	Notes:
	+
	+	* For security reasons direct browsing of windows shares only works in Microsoft Internet Explorer per default (and only in the "local zone").
	+	* For Mozilla and Firefox it can be enabled through different workaround mentioned in the [[http://kb.mozillazine.org/Links_to_local_pages_do_not_work\|Mozilla Knowledge Base]]. However, there will still be a JavaScript warning about trying to open a Windows Share. To remove this warning (for all users), put the following line in ''conf/lang/en/lang.php'' (more details at [[doku>localization#changing_some_localized_texts_and_strings_in_your_installation\|localization]]): <code - conf/lang/en/lang.php>
	+	<?php
	+	/**
	+	* Customization of the english language file
	+	* Copy only the strings that needs to be modified
	+	*/
	+	$lang['js']['nosmblinks'] = '';
	+	</code>
	+
	+	==== Image Links ====
	+
	+	You can also use an image to link to another internal or external page by combining the syntax for links and [[#images_and_other_files\|images]] (see below) like this:
	+
	+	[[http://php.net\|{{wiki:dokuwiki-128.png}}]]
	+
	+	[[http://php.net\|{{wiki:dokuwiki-128.png}}]]
	+
	+	Please note: The image formatting is the only formatting syntax accepted in link names.
	+
	+	The whole [[#images_and_other_files\|image]] and [[#links\|link]] syntax is supported (including image resizing, internal and external images and URLs and interwiki links).
	+
	+	===== Footnotes =====
	+
	+	You can add footnotes ((This is a footnote)) by using double parentheses.
	+
	+	You can add footnotes ((This is a footnote)) by using double parentheses.
	+
	+	===== Sectioning =====
	+
	+	You can use up to five different levels of headlines to structure your content. If you have more than three headlines, a table of contents is generated automatically -- this can be disabled by including the string ''<nowiki>~~NOTOC~~</nowiki>'' in the document.
	+
	+	==== Headline Level 3 ====
	+	=== Headline Level 4 ===
	+	== Headline Level 5 ==
	+
	+	==== Headline Level 3 ====
	+	=== Headline Level 4 ===
	+	== Headline Level 5 ==
	+
	+	By using four or more dashes, you can make a horizontal line:
	+
	+	----
	+
	+	===== Media Files =====
	+
	+	You can include external and internal [[doku>images\|images, videos and audio files]] with curly brackets. Optionally you can specify the size of them.
	+
	+	Real size: {{wiki:dokuwiki-128.png}}
	+
	+	Resize to given width: {{wiki:dokuwiki-128.png?50}}
	+
	+	Resize to given width and height((when the aspect ratio of the given width and height doesn't match that of the image, it will be cropped to the new ratio before resizing)): {{wiki:dokuwiki-128.png?200x50}}
	+
	+	Resized external image: {{https://www.php.net/images/php.gif?200x50}}
	+
	+	Real size: {{wiki:dokuwiki-128.png}}
	+	Resize to given width: {{wiki:dokuwiki-128.png?50}}
	+	Resize to given width and height: {{wiki:dokuwiki-128.png?200x50}}
	+	Resized external image: {{https://www.php.net/images/php.gif?200x50}}
	+
	+
	+	By using left or right whitespaces you can choose the alignment.
	+
	+	{{ wiki:dokuwiki-128.png}}
	+
	+	{{wiki:dokuwiki-128.png }}
	+
	+	{{ wiki:dokuwiki-128.png }}
	+
	+	{{ wiki:dokuwiki-128.png}}
	+	{{wiki:dokuwiki-128.png }}
	+	{{ wiki:dokuwiki-128.png }}
	+
	+	Of course, you can add a title (displayed as a tooltip by most browsers), too.
	+
	+	{{ wiki:dokuwiki-128.png \|This is the caption}}
	+
	+	{{ wiki:dokuwiki-128.png \|This is the caption}}
	+
	+	For linking an image to another page see [[#Image Links]] above.
	+
	+	==== Supported Media Formats ====
	+
	+	DokuWiki can embed the following media formats directly.
	+
	+	\| Image \| ''gif'', ''jpg'', ''png'' \|
	+	\| Video \| ''webm'', ''ogv'', ''mp4'' \|
	+	\| Audio \| ''ogg'', ''mp3'', ''wav'' \|
	+	\| Flash \| ''swf'' \|
	+
	+	If you specify a filename that is not a supported media format, then it will be displayed as a link instead.
	+
	+	By adding ''?linkonly'' you provide a link to the media without displaying it inline
	+
	+	{{wiki:dokuwiki-128.png?linkonly}}
	+
	+	{{wiki:dokuwiki-128.png?linkonly}} This is just a link to the image.
	+
	+	==== Fallback Formats ====
	+
	+	Unfortunately not all browsers understand all video and audio formats. To mitigate the problem, you can upload your file in different formats for maximum browser compatibility.
	+
	+	For example consider this embedded mp4 video:
	+
	+	{{video.mp4\|A funny video}}
	+
	+	When you upload a ''video.webm'' and ''video.ogv'' next to the referenced ''video.mp4'', DokuWiki will automatically add them as alternatives so that one of the three files is understood by your browser.
	+
	+	Additionally DokuWiki supports a "poster" image which will be shown before the video has started. That image needs to have the same filename as the video and be either a jpg or png file. In the example above a ''video.jpg'' file would work.
	+
	+	===== Lists =====
	+
	+	Dokuwiki supports ordered and unordered lists. To create a list item, indent your text by two spaces and use a ''*'' for unordered lists or a ''-'' for ordered ones.
	+
	+	* This is a list
	+	* The second item
	+	* You may have different levels
	+	* Another item
	+
	+	- The same list but ordered
	+	- Another item
	+	- Just use indention for deeper levels
	+	- That's it
	+
	+	<code>
	+	* This is a list
	+	* The second item
	+	* You may have different levels
	+	* Another item
	+
	+	- The same list but ordered
	+	- Another item
	+	- Just use indention for deeper levels
	+	- That's it
	+	</code>
	+
	+	Also take a look at the [[doku>faq:lists\|FAQ on list items]].
	+
	+	===== Text Conversions =====
	+
	+	DokuWiki can convert certain pre-defined characters or strings into images or other text or HTML.
	+
	+	The text to image conversion is mainly done for smileys. And the text to HTML conversion is used for typography replacements, but can be configured to use other HTML as well.
	+
	+	==== Text to Image Conversions ====
	+
	+	DokuWiki converts commonly used [[wp>emoticon]]s to their graphical equivalents. Those [[doku>Smileys]] and other images can be configured and extended. Here is an overview of Smileys included in DokuWiki:
	+
	+	* 8-) %% 8-) %%
	+	* 8-O %% 8-O %%
	+	* :-( %% :-( %%
	+	* :-) %% :-) %%
	+	* =) %% =) %%
	+	* :-/ %% :-/ %%
	+	* :-\ %% :-\ %%
	+	* :-? %% :-? %%
	+	* :-D %% :-D %%
	+	* :-P %% :-P %%
	+	* :-O %% :-O %%
	+	* :-X %% :-X %%
	+	* :-\| %% :-\| %%
	+	* ;-) %% ;-) %%
	+	* ^_^ %% ^_^ %%
	+	* m( %% m( %%
	+	* :?: %% :?: %%
	+	* :!: %% :!: %%
	+	* LOL %% LOL %%
	+	* FIXME %% FIXME %%
	+	* DELETEME %% DELETEME %%
	+
	+	==== Text to HTML Conversions ====
	+
	+	Typography: [[DokuWiki]] can convert simple text characters to their typographically correct entities. Here is an example of recognized characters.
	+
	+	-> <- <-> => <= <=> >> << -- --- 640x480 (c) (tm) (r)
	+	"He thought 'It's a man's world'..."
	+
	+	<code>
	+	-> <- <-> => <= <=> >> << -- --- 640x480 (c) (tm) (r)
	+	"He thought 'It's a man's world'..."
	+	</code>
	+
	+	The same can be done to produce any kind of HTML, it just needs to be added to the [[doku>entities\|pattern file]].
	+
	+	There are three exceptions which do not come from that pattern file: multiplication entity (640x480), 'single' and "double quotes". They can be turned off through a [[doku>config:typography\|config option]].
	+
	+	===== Quoting =====
	+
	+	Some times you want to mark some text to show it's a reply or comment. You can use the following syntax:
	+
	+	<code>
	+	I think we should do it
	+
	+	> No we shouldn't
	+
	+	>> Well, I say we should
	+
	+	> Really?
	+
	+	>> Yes!
	+
	+	>>> Then lets do it!
	+	</code>
	+
	+	I think we should do it
	+
	+	> No we shouldn't
	+
	+	>> Well, I say we should
	+
	+	> Really?
	+
	+	>> Yes!
	+
	+	>>> Then lets do it!
	+
	+	===== Tables =====
	+
	+	DokuWiki supports a simple syntax to create tables.
	+
	+	^ Heading 1 ^ Heading 2 ^ Heading 3 ^
	+	\| Row 1 Col 1 \| Row 1 Col 2 \| Row 1 Col 3 \|
	+	\| Row 2 Col 1 \| some colspan (note the double pipe) \|\|
	+	\| Row 3 Col 1 \| Row 3 Col 2 \| Row 3 Col 3 \|
	+
	+	Table rows have to start and end with a ''\|'' for normal rows or a ''^'' for headers.
	+
	+	^ Heading 1 ^ Heading 2 ^ Heading 3 ^
	+	\| Row 1 Col 1 \| Row 1 Col 2 \| Row 1 Col 3 \|
	+	\| Row 2 Col 1 \| some colspan (note the double pipe) \|\|
	+	\| Row 3 Col 1 \| Row 3 Col 2 \| Row 3 Col 3 \|
	+
	+	To connect cells horizontally, just make the next cell completely empty as shown above. Be sure to have always the same amount of cell separators!
	+
	+	Vertical tableheaders are possible, too.
	+
	+	\| ^ Heading 1 ^ Heading 2 ^
	+	^ Heading 3 \| Row 1 Col 2 \| Row 1 Col 3 \|
	+	^ Heading 4 \| no colspan this time \| \|
	+	^ Heading 5 \| Row 2 Col 2 \| Row 2 Col 3 \|
	+
	+	As you can see, it's the cell separator before a cell which decides about the formatting:
	+
	+	\| ^ Heading 1 ^ Heading 2 ^
	+	^ Heading 3 \| Row 1 Col 2 \| Row 1 Col 3 \|
	+	^ Heading 4 \| no colspan this time \| \|
	+	^ Heading 5 \| Row 2 Col 2 \| Row 2 Col 3 \|
	+
	+	You can have rowspans (vertically connected cells) by adding ''%%:::%%'' into the cells below the one to which they should connect.
	+
	+	^ Heading 1 ^ Heading 2 ^ Heading 3 ^
	+	\| Row 1 Col 1 \| this cell spans vertically \| Row 1 Col 3 \|
	+	\| Row 2 Col 1 \| ::: \| Row 2 Col 3 \|
	+	\| Row 3 Col 1 \| ::: \| Row 2 Col 3 \|
	+
	+	Apart from the rowspan syntax those cells should not contain anything else.
	+
	+	^ Heading 1 ^ Heading 2 ^ Heading 3 ^
	+	\| Row 1 Col 1 \| this cell spans vertically \| Row 1 Col 3 \|
	+	\| Row 2 Col 1 \| ::: \| Row 2 Col 3 \|
	+	\| Row 3 Col 1 \| ::: \| Row 2 Col 3 \|
	+
	+	You can align the table contents, too. Just add at least two whitespaces at the opposite end of your text: Add two spaces on the left to align right, two spaces on the right to align left and two spaces at least at both ends for centered text.
	+
	+	^ Table with alignment ^^^
	+	\| right\| center \|left \|
	+	\|left \| right\| center \|
	+	\| xxxxxxxxxxxx \| xxxxxxxxxxxx \| xxxxxxxxxxxx \|
	+
	+	This is how it looks in the source:
	+
	+	^ Table with alignment ^^^
	+	\| right\| center \|left \|
	+	\|left \| right\| center \|
	+	\| xxxxxxxxxxxx \| xxxxxxxxxxxx \| xxxxxxxxxxxx \|
	+
	+	Note: Vertical alignment is not supported.
	+
	+	===== No Formatting =====
	+
	+	If you need to display text exactly like it is typed (without any formatting), enclose the area either with ''%%<nowiki>%%'' tags or even simpler, with double percent signs ''<nowiki>%%</nowiki>''.
	+
	+	<nowiki>
	+	This is some text which contains addresses like this: http://www.splitbrain.org and formatting, but nothing is done with it.
	+	</nowiki>
	+	The same is true for %%//__this__ text// with a smiley ;-)%%.
	+
	+	<nowiki>
	+	This is some text which contains addresses like this: http://www.splitbrain.org and formatting, but nothing is done with it.
	+	</nowiki>
	+	The same is true for %%//__this__ text// with a smiley ;-)%%.
	+
	+	===== Code Blocks =====
	+
	+	You can include code blocks into your documents by either indenting them by at least two spaces (like used for the previous examples) or by using the tags ''%%<code>%%'' or ''%%<file>%%''.
	+
	+	This is text is indented by two spaces.
	+
	+	<code>
	+	This is preformatted code all spaces are preserved: like <-this
	+	</code>
	+
	+	<file>
	+	This is pretty much the same, but you could use it to show that you quoted a file.
	+	</file>
	+
	+	Those blocks were created by this source:
	+
	+	This is text is indented by two spaces.
	+
	+	<code>
	+	This is preformatted code all spaces are preserved: like <-this
	+	</code>
	+
	+	<file>
	+	This is pretty much the same, but you could use it to show that you quoted a file.
	+	</file>
	+
	+	==== Syntax Highlighting ====
	+
	+	[[wiki:DokuWiki]] can highlight sourcecode, which makes it easier to read. It uses the [[http://qbnz.com/highlighter/\|GeSHi]] Generic Syntax Highlighter -- so any language supported by GeSHi is supported. The syntax uses the same code and file blocks described in the previous section, but this time the name of the language syntax to be highlighted is included inside the tag, e.g. ''<nowiki><code java></nowiki>'' or ''<nowiki><file java></nowiki>''.
	+
	+	<code java>
	+	/**
	+	* The HelloWorldApp class implements an application that
	+	* simply displays "Hello World!" to the standard output.
	+	*/
	+	class HelloWorldApp {
	+	public static void main(String[] args) {
	+	System.out.println("Hello World!"); //Display the string.
	+	}
	+	}
	+	</code>
	+
	+	The following language strings are currently recognized: //4cs 6502acme 6502kickass 6502tasm 68000devpac abap actionscript3 actionscript ada aimms algol68 apache applescript apt_sources arm asm asp asymptote autoconf autohotkey autoit avisynth awk bascomavr bash basic4gl batch bf biblatex bibtex blitzbasic bnf boo caddcl cadlisp ceylon cfdg cfm chaiscript chapel cil c_loadrunner clojure c_mac cmake cobol coffeescript c cpp cpp-qt cpp-winapi csharp css cuesheet c_winapi dart dcl dcpu16 dcs delphi diff div dos dot d ecmascript eiffel email epc e erlang euphoria ezt f1 falcon fo fortran freebasic freeswitch fsharp gambas gdb genero genie gettext glsl gml gnuplot go groovy gwbasic haskell haxe hicest hq9plus html html4strict html5 icon idl ini inno intercal io ispfpanel java5 java javascript jcl j jquery julia kixtart klonec klonecpp kotlin latex lb ldif lisp llvm locobasic logtalk lolcode lotusformulas lotusscript lscript lsl2 lua m68k magiksf make mapbasic mathematica matlab mercury metapost mirc mk-61 mmix modula2 modula3 mpasm mxml mysql nagios netrexx newlisp nginx nimrod nsis oberon2 objc objeck ocaml-brief ocaml octave oobas oorexx oracle11 oracle8 oxygene oz parasail parigp pascal pcre perl6 perl per pf phix php-brief php pic16 pike pixelbender pli plsql postgresql postscript povray powerbuilder powershell proftpd progress prolog properties providex purebasic pycon pys60 python qbasic qml q racket rails rbs rebol reg rexx robots roff rpmspec rsplus ruby rust sas sass scala scheme scilab scl sdlbasic smalltalk smarty spark sparql sql sshconfig standardml stonescript swift systemverilog tclegg tcl teraterm texgraph text thinbasic tsql twig typoscript unicon upc urbi uscript vala vbnet vb vbscript vedit verilog vhdl vim visualfoxpro visualprolog whitespace whois winbatch wolfram xbasic xml xojo xorg_conf xpp yaml z80 zxbasic//
	+
	+	There are additional [[doku>syntax_highlighting\|advanced options]] available for syntax highlighting, such as highlighting lines or adding line numbers.
	+
	+	==== Downloadable Code Blocks ====
	+
	+	When you use the ''%%<code>%%'' or ''%%<file>%%'' syntax as above, you might want to make the shown code available for download as well. You can do this by specifying a file name after language code like this:
	+
	+	<code>
	+	<file php myexample.php>
	+	<?php echo "hello world!"; ?>
	+	</file>
	+	</code>
	+
	+	<file php myexample.php>
	+	<?php echo "hello world!"; ?>
	+	</file>
	+
	+	If you don't want any highlighting but want a downloadable file, specify a dash (''-'') as the language code: ''%%<code - myfile.foo>%%''.
	+
	+	===== RSS/ATOM Feed Aggregation =====
	+	[[DokuWiki]] can integrate data from external XML feeds. For parsing the XML feeds, [[http://simplepie.org/\|SimplePie]] is used. All formats understood by SimplePie can be used in DokuWiki as well. You can influence the rendering by multiple additional space separated parameters:
	+
	+	^ Parameter ^ Description ^
	+	\| any number \| will be used as maximum number items to show, defaults to 8 \|
	+	\| reverse \| display the last items in the feed first \|
	+	\| author \| show item authors names \|
	+	\| date \| show item dates \|
	+	\| description\| show the item description. All HTML tags will be stripped \|
	+	\| nosort \| do not sort the items in the feed \|
	+	\| //n//[dhm] \| refresh period, where d=days, h=hours, m=minutes. (e.g. 12h = 12 hours). \|
	+
	+	The refresh period defaults to 4 hours. Any value below 10 minutes will be treated as 10 minutes. [[wiki:DokuWiki]] will generally try to supply a cached version of a page, obviously this is inappropriate when the page contains dynamic external content. The parameter tells [[wiki:DokuWiki]] to re-render the page if it is more than //refresh period// since the page was last rendered.
	+
	+	By default the feed will be sorted by date, newest items first. You can sort it by oldest first using the ''reverse'' parameter, or display the feed as is with ''nosort''.
	+
	+	Example:
	+
	+	{{rss>http://slashdot.org/index.rss 5 author date 1h }}
	+
	+	{{rss>http://slashdot.org/index.rss 5 author date 1h }}
	+
	+
	+	===== Control Macros =====
	+
	+	Some syntax influences how DokuWiki renders a page without creating any output it self. The following control macros are availble:
	+
	+	^ Macro ^ Description \|
	+	\| %%~~NOTOC~~%% \| If this macro is found on the page, no table of contents will be created \|
	+	\| %%~~NOCACHE~~%% \| DokuWiki caches all output by default. Sometimes this might not be wanted (eg. when the %%<php>%% syntax above is used), adding this macro will force DokuWiki to rerender a page on every call \|
	+
	+	===== Syntax Plugins =====
	+
	+	DokuWiki's syntax can be extended by [[doku>plugins\|Plugins]]. How the installed plugins are used is described on their appropriate description pages. The following syntax plugins are available in this particular DokuWiki installation:
	+
	+	~~INFO:syntaxplugins~~

2026/05/02 16:29	current
Line 1:	Line 1:
	+	====== DokuWiki ======
	+
	+	[[doku>wiki:dokuwiki\|{{wiki:dokuwiki-128.png }}]] DokuWiki is a simple to use and highly versatile Open Source [[wp>wiki]] software that doesn't require a database. It is loved by users for its clean and readable [[wiki:syntax]]. The ease of maintenance, backup and integration makes it an administrator's favorite. Built in [[doku>acl\|access controls]] and [[doku>auth\|authentication connectors]] make DokuWiki especially useful in the enterprise context and the large number of [[doku>plugins]] contributed by its vibrant community allow for a broad range of use cases beyond a traditional wiki.
	+
	+	Read the [[doku>manual\|DokuWiki Manual]] to unleash the full power of DokuWiki.
	+
	+	===== Download =====
	+
	+	DokuWiki is available at https://download.dokuwiki.org/
	+
	+
	+	===== Read More =====
	+
	+	All documentation and additional information besides the [[syntax\|syntax description]] is maintained in the DokuWiki at [[doku>\|www.dokuwiki.org]].
	+
	+	About DokuWiki
	+
	+	* [[doku>features\|A feature list]] :!:
	+	* [[doku>users\|Happy Users]]
	+	* [[doku>press\|Who wrote about it]]
	+	* [[doku>blogroll\|What Bloggers think]]
	+	* [[https://www.wikimatrix.org/show/DokuWiki\|Compare it with other wiki software]]
	+
	+	Installing DokuWiki
	+
	+	* [[doku>requirements\|System Requirements]]
	+	* [[https://download.dokuwiki.org/\|Download DokuWiki]] :!:
	+	* [[doku>changes\|Change Log]]
	+	* [[doku>Install\|How to install or upgrade]] :!:
	+	* [[doku>config\|Configuration]]
	+
	+	Using DokuWiki
	+
	+	* [[doku>syntax\|Wiki Syntax]]
	+	* [[doku>manual\|The manual]] :!:
	+	* [[doku>FAQ\|Frequently Asked Questions (FAQ)]]
	+	* [[doku>glossary\|Glossary]]
	+
	+	Customizing DokuWiki
	+
	+	* [[doku>tips\|Tips and Tricks]]
	+	* [[doku>Template\|How to create and use templates]]
	+	* [[doku>plugins\|Installing plugins]]
	+	* [[doku>development\|Development Resources]]
	+
	+	DokuWiki Feedback and Community
	+
	+	* [[doku>newsletter\|Subscribe to the newsletter]] :!:
	+	* [[doku>mailinglist\|Join the mailing list]]
	+	* [[https://forum.dokuwiki.org\|Check out the user forum]]
	+	* [[doku>irc\|Talk to other users in the IRC channel]]
	+	* [[https://github.com/splitbrain/dokuwiki/issues\|Submit bugs and feature wishes]]
	+	* [[doku>thanks\|Some humble thanks]]
	+
	+
	+	===== Copyright =====
	+
	+	2004-2020 (c) Andreas Gohr <andi@splitbrain.org>((Please do not contact me for help and support -- use the [[doku>mailinglist]] or [[https://forum.dokuwiki.org\|forum]] instead)) and the DokuWiki Community
	+
	+	The DokuWiki engine is licensed under [[https://www.gnu.org/licenses/gpl.html\|GNU General Public License]] Version 2. If you use DokuWiki in your company, consider [[doku>donate\|donating]] a few bucks ;-).
	+
	+	Not sure what this means? See the [[doku>faq:license\|FAQ on the Licenses]].