downloads:frap_analysis
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+ | ~~NOTOC~~ | ||
+ | [{{ http:// | ||
+ | ====== FrapCalc ====== | ||
+ | **Please jump to [[https:// | ||
+ | |||
+ | /** | ||
+ | |||
+ | Analyze FRAP curves and get parameter by curve fitting ([[http:// | ||
+ | |||
+ | ===== Author ===== | ||
+ | |||
+ | Kota Miura\\ | ||
+ | Centre for Molecular and Cellular Imaging (CMCI)\\ | ||
+ | EMBL Heidelberg\\ | ||
+ | miura at embl dot de\\ | ||
+ | Tel: +49 6221 387 404 | ||
+ | ===== Questions & Comments ===== | ||
+ | ? | ||
+ | Please post in the commenting section below at the bottom of this page | ||
+ | |||
+ | |||
+ | |||
+ | ===== Source ===== | ||
+ | |||
+ | Released under the GNU General Public License. | ||
+ | |||
+ | ===== Requires ===== | ||
+ | |||
+ | IgorPro ver 5 or higher ([[http:// | ||
+ | ===== Installation ===== | ||
+ | |||
+ | Download [[http:// | ||
+ | |||
+ | ===== Description ===== | ||
+ | |||
+ | Analyze FRAP curves to derive recovery parameters. | ||
+ | |||
+ | ===== Features ===== | ||
+ | |||
+ | * Import FRAP measurement tab-delimited text files of Zeiss data format (6 different data structures)\\ Leica data format (7 different data structures) - Three different ways of normalizing FRAP curve - Curve fitting by single and double exponential formula and 2 diffusion formula. | ||
+ | * Correction for the acquisition bleaching. | ||
+ | * Output of half-max, diffusion coefficient, | ||
+ | * Weighting for the fitting. | ||
+ | * Evaluation of goodness of fit by chi-square and gamma function. | ||
+ | * Graphing of the fitted curve and estimation curve without acquisition bleaching. | ||
+ | * Batch Fitting | ||
+ | |||
+ | ===== Papers + Misc ===== | ||
+ | |||
+ | ==== Papers using this script ==== | ||
+ | * Runz, H. et al., 2006. Sterols regulate ER-export dynamics of secretory cargo protein ts-O45-G. The EMBO journal, 25(13), p.2953-65. [[http:// | ||
+ | * Atlason, P.T. et al., 2007. N-Methyl-D-aspartate (NMDA) receptor subunit NR1 forms the substrate for oligomeric assembly of the NMDA receptor. The Journal of biological chemistry, 282(35), p.25299-307. [[http:// | ||
+ | * Pooler, A.M. & McIlhinney, R.A.J., 2007. Lateral diffusion of the GABAB receptor is regulated by the GABAB2 C terminus. The Journal of biological chemistry, 282(35), p.25349-56. [[http:// | ||
+ | * Hoppa, M.B. et al., 2009. Chronic palmitate exposure inhibits insulin secretion by dissociation of Ca(2+) channels from secretory granules. Cell metabolism, 10(6), p.455-65. [[http:// | ||
+ | * Treeck, M. et al., 2009. Functional analysis of the leading malaria vaccine candidate AMA-1 reveals an essential role for the cytoplasmic domain in the invasion process. PLoS pathogens, 5(3), p.e1000322. [[http:// | ||
+ | * Bancaud, A., Huet, S., Rabut, G., Ellenberg, J., 2010. Fluorescence perturbation techniques to study mobility and molecular dynamics of proteins in live cells: FRAP, photoactivation, | ||
+ | * Bosch-Presegué, | ||
+ | * Caillier, B. et al., 2011. QRS widening and QT prolongation under bupropion: a unique cardiac electrophysiological profile. Fundamental & clinical pharmacology. [[http:// | ||
+ | * Díaz, A. et al., 2011. Processivity and subcellular localization of glycogen synthase depend on a non-catalytic high affinity glycogen-binding site. The Journal of biological chemistry, 286(21), p.18505-14. [[http:// | ||
+ | * Coutinho-Budd J, Ghukasyan V, Zylka MJ, Polleux F. The F-BAR domains from srGAP1, srGAP2 and srGAP3 regulate membrane deformation differently. Journal of cell science. 2012;125(Pt 14): | ||
+ | ... searches were done by google hits, so if YOURS is missing please tell me! | ||
+ | ==== Web Back Links ==== | ||
+ | |||
+ | * [[http:// | ||
+ | * [[http:// | ||
+ | * MatLab-migrated version of FRAPCalc. | ||
+ | * [[http:// | ||
+ | * [[http:// | ||
+ | * [[http:// | ||
+ | * Dissertation using FRAPCalc | ||
+ | * [[http:// | ||
+ | |||
+ | |||
+ | ===== History ===== | ||
+ | |||
+ | * 05-9-9 | ||
+ | * 1st version | ||
+ | * 07-3-28 | ||
+ | * 9th version | ||
+ | * 07-8-27 ver 9a | ||
+ | * Added Leica new file format importing (csv format) | ||
+ | * Made K_SoumpasisHalfLife2(fitwave, | ||
+ | * 07-10-30 ver9b | ||
+ | * For details, read the [[http:// | ||
+ | * 08-03-25 ver 9c | ||
+ | * For details see the [[http:// | ||
+ | * 08-07-24 ver 9e | ||
+ | * Added two data set types for importing. Olympus .cvs file is now possible. | ||
+ | * 08-10-07 ver9f | ||
+ | * Added Excel file importing funciton (Four column, with Time-Frap-All Cell- Base, with the first line containg column name) and tab-delimited text file. | ||
+ | * 08/12/11 ver9g | ||
+ | * Replaced fitting function for double-exponential fitting, follwoing the recommendation of wavemetrics. | ||
+ | * Half-time estimation for double exponential fitting had a bug, when data range is below the half-max intensity. This is now done by extrapolation. | ||
+ | * 09-10-26 ver9h | ||
+ | * Fitted parameters appear in plot legend even when mobile fraction >1.0. (C. Tischer' | ||
+ | * Added documentation for gammaQ=1 cases. See -> 2.7. [[http:// | ||
+ | * 10-03-03 ver9j | ||
+ | * Batch Processing funciton with averaging function (request from N. Goldsimth). See additional explanation in the [[documents: | ||
+ | * K_FrapCalcCore() was modified so that averaged curve could be fitted as well. Since averaged curve does not have original normalizaton process is not required but then several parameters which are calculated during normalization will be missing. For this, flag " | ||
+ | * getAverageGApRatio(Gfilelist): | ||
+ | * Fitting of averaged curve is done with actual standard deviation | ||
+ | * BatchFitting() was added to the last line of BatchAverageAndFit() | ||
+ | |||
+ | |||
+ | */ |
downloads/frap_analysis.txt · Last modified: 2017/05/11 15:28 by kota