App for 2015 elife paper

GloFish

This page provides links to and brief introduction to an app written by Sean Gillespie to fit data on GFP and huDys-GFP in muscle fibres in live zebrafish embryos (2dpf), although it will also work for other studies of 1D diffusion in cells. The data on zebfrafish embryos was obtained by Dr Fernanda Bajanca, working in the lab of Prof Simon Hughes at KCL. The app folder includes a single data set for GFP in zebrafish embryo muscle cell, to help with testing that the app works. This data was obtained by Fernanda Bajanca at KCL. The diffusion model was developed by Vinicio Gonzalez-Perez, Richard Sear and Sean Gillespie.

Sean Gillespie wrote the app in the summer of 2012. He was funded by an EPSRC Vacation Bursary. We thank EPSRC for this support.

The app allows the user to fit a model for 1D diffusion with a constant diffusion constant, D, more-or-less directly to the data output by a confocal microscope. No programming is required, but some knowledge of the basic physics of diffusion is required to use it sensibly, and to interpret the results.


How to download and run

Zip file for (pre-built) Windows version is here. Once unzipped, the folder contains a file ‘FRAP_APP.exe’ which should just run straightaway on a Windows machine.

Gzipped tar file for Linux is here.

Should work on Windows (tested on Windows 7, may work on other versions). Tested on a reasonably uptodate version of Ubuntu Linux at Surrey, should work on other versions but of course it relies on Qt on the machine etc.

Both the Windows and Linux versions contain a sub-folder “sample_data_G113” which contains data for one fiber expressing GFP: 200 successive images + “intensity.txt” which is required for the 200 image acquisition times. The file “case_parameters.in” has values for the bleach position etc. This GFP data set is one used in the paper.

Linux instructions

Once you have uncompressed the file. Go into the SOURCE directory. Type “qmake-qt4” return. Type “make” return. Go into BUILD directory. Type “FRAP_APP”. Window should pop up and you are in business.

Once the app is running then hit the load data button and select the “sample_data_G113” directory, then open. As the parameter values for data set G113 (which is the set in Fig. 1d and f of the paper) are already set it should fit first time. Select “Fit centre” to fit in the same way as in the paper. You should then get the same best-fit values as in the paper, e.g., the diffusion constant should be 9.0, to one decimal place, (in micrometres squared/s). Note that the app will fit in various ways, e.g., with beta set equal to 0, with and without fitting the centre of the Gaussian etc. Most of these ways are not in the paper, and are also are not documented. Sorry. Use at your own risk!

Also, unfortunately the builtin help may not work in Linux, but it will appear in a window if in the BUILD directory, you type “assistant-qt4 -collectionFile help.qhc” return. Note that the help is not comprehensive. It was written as a project over the summer and this is what we had time to do.

Windows instructions

Just unzip and run the FRAP_APP.exe executable. App should run as in Linux instructions, except the help should work directly from the app. As with the Linux version you can fit the suppied GFP data set, and should get the parameter values in the paper.

Problems?

If the app does not work on your machine then that is likely to be a compatibility issue that I can’t help with. If it runs but the results are not what you expect, I may be able to help, so you can drop me an email. Note that Sean Gillespie wrote it in 2012 as an undergraduate and is now doing a PhD in an unrelated field, i.e., has moved in his life. If you have a question about the experimental data, then you should contact Fernanda Bajanca or Simon Hughes. Fernanda did the experiments, mostly in Simon’s labs.

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