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EMBL BioImage Data Analysis

EuBIAS

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EMBL Heidelberg
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Timeline of @cmci_

cmci_ avatar

RT @naivelocus: Quantitating the cell: turning images into numbers with ImageJ https://t.co/kAKeCEJbnW
About 1 day, 15 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @AssafZaritsky: Quantifying inhomogeneity of spatial point pattern distributions, https://t.co/a8O5uhSaT5 . ImageJ/Fiji plugin available!…
About 2 days, 10 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

I sometimes get secret inquiry from editors to check image manipulations, but I think it's better be in the hand of the whole community.
About 3 days, 10 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @PubPeer: Our Boris Barbour responds to pesky anonymous critics at @NatureNews: https://t.co/vbdMCd1Xr3
About 3 days, 10 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

[pls spread] Travel grant for bioimage analysis: application closing soon! https://t.co/hb62M6nkhO Skill up in other country! #NEUBIAS
About 5 days, 2 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

These are two different bioimage analysis school, one very advanced, on for beginners, by the way.
About 5 days, 2 hours ago by: Kota Miura (@cmci_)
downloads:frap_analysis
image069.jpg

FrapCalc

Analyze FRAP curves and get parameter by curve fitting (documentation.). Lecture notes are also available ( Lecture Notes (Apr. 2010))

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 (IgorPro, Wavemetrics).

Installation

Download K_FRAPcalcV9k.ipf to a place where you can access easily (you might need to right click or ctrl-click and then save it to your local machine). Open the file in IgorPro and compile.

Description

Analyze FRAP curves to derive recovery parameters. More details are in the documentation.

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, mobile/immobile fractions.
  • 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. Accessed February 7, 2012.
  • 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. Accessed February 7, 2012.
  • 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. Accessed February 7, 2012.
  • 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. Accessed February 7, 2012.
  • 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. Accessed February 7, 2012.
  • 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, photoconversion, and FLIP. Cold Spring Harb. Protoc. 2010, pdb.top90.
  • Bosch-Presegué, L. et al., 2011. Stabilization of Suv39H1 by SirT1 is part of oxidative stress response and ensures genome protection. Molecular cell, 42(2), p.210-23. Accessed January 30, 2012.
  • Caillier, B. et al., 2011. QRS widening and QT prolongation under bupropion: a unique cardiac electrophysiological profile. Fundamental & clinical pharmacology. Accessed February 7, 2012.
  • 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. Accessed February 7, 2012.
  • 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):3390–401. Accessed October 10, 2012.

… searches were done by google hits, so if YOURS is missing please tell me!

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,amplitude) for calculateing Half max. Previous one had problem when point 1 is larger than 0.5 ? Changes for the texts in the graph (Half max value added to diffusion fittings) see more details in the code.
  • 07-10-30 ver9b
    • For details, read the blog
  • 08-03-25 ver 9c
  • 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
  • 10-03-03 ver9j
    • Batch Processing funciton with averaging function (request from N. Goldsimth). See additional explanation in the documentation page
    • 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 “G_doAveraged” was added
    • getAverageGApRatio(Gfilelist): Gap Ratio is calculated by averaging individual
    • 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: 2016/05/24 05:46 (external edit)