A GUI for plate reader growth curve analyses
- 2 files
- 13 downloads
A GUI for the analysis of plate reader growth curve results:
1. Automatic calculation of the average of a few wells (repetitions)
2. Plotting of the average + standard deviation of OD, reporter, or reporter to OD ratio, with ability to control the color and line properties of each group, which group to display, the limits of the plot, and an option to display each well separately
3. Defining a blank group or subtracting a constant value
4. Load settings from previously saved sessions
This GUI was built with the aid of the 'GUI layout toolbox' (file exchange submission, see link below), and it is required for its functionality, download it and run the 'install.m' file there.
Please, help to improve it:
1. Report any bug or inconvenience you experience.
2. Make suggestions on how to improve it.
3. Modify the code and share what you changed.
Cite As
Nitai Steinberg (2020). A GUI for plate reader growth curve analyses (https://www.mathworks.com/matlabcentral/fileexchange/43595-a-gui-for-plate-reader-growth-curve-analyses), MATLAB Central File Exchange. Retrieved .
Comments and Ratings (8)
Updates
| 1.10.0.0 | The GUI layout toolbox has two versions
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| 1.10.0.0 | The GUI layout toolbox has two versions
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| 1.10.0.0 | There was a bug in the Excel export option, it was now fixed |
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| 1.9.0.0 | There is now option to export the results to Excel |
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| 1.8.0.0 | A small bug was fixed (import from excel of a plate layout that contain group names that are only numbers is now possible) |
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| 1.7.0.0 | A bug causing it not to save when asked whether to save in the end of the session was fixed |
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| 1.6.0.0 | A few bugs regarding plate layout definition were fixed |
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| 1.5.0.0 | A few bugs corrected + an option to load a layout from an Excel sheet (to be better compatible with previous version) |
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| 1.4.0.0 | Definition of the plate layout is now done in the GUI itself. The new version will not open sessions that were saved in the older version. But there is a new option to copy the plate layout and plot settings from old sessions so it is not much work |
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| 1.1.0.0 | Some bugs were fixed:
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MATLAB Release Compatibility
Platform Compatibility
Windows macOS LinuxTags
Acknowledgements
Inspired by: GUI Layout Toolbox, GUI Layout Toolbox
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Andres Florez (view profile)
Hi Nitai,
Amazing tool!, has made my plotting very efficient, faster and accurate. I was wondering, have you thought of having an extra function to normalize by the initial OD?, meaning take the first time point and normalize the other time points by it?, because sometimes I don't manage to have the same OD for all my conditions, so that would be handy. Also what about using a shadow instead of error bars?.
Athanasios Tsagkadouras (view profile)
silvia chuartzman (view profile)
Hi Nitai
I downloaded your script together with the Gui layout toolbox/
I try to run readPlate but it doesn't recognize buildfcn .
What is the problem?
thanks
Silvia
Nitai Steinberg (view profile)
Hello Jessika,
Thank you for your comments.
I am afraid (not sure) that it is a problem in running the xlswrite function in the Mac OS. See this discussion:
http://www.mathworks.com/matlabcentral/answers/87657-error-in-exporting-values-using-xlswrite
And this function that maybe can fix it: (you will need to incorporate it into the code...)
http://www.mathworks.com/matlabcentral/fileexchange/37560-xlwrite---export-data-to-excel-from-matlab-on-mac-win
Can you try it on PC to see if you get the same error?
About the AUC, I am not sure I am going to add it in the near future but if anybody wants to help and improve this app, they are more than welcome!
Jessika (view profile)
Hello Nitai,
Pretty nice app, I'm using it to draw my curves and it works pretty well (thanks!), however I'm getting an error message when I try to export to excel (see below, I'm on Mac). Also it'd be interesting to get the data of the Growth rates and AUC.
Thanks a lot for the app and your future help!
Warning: Could not start Excel server for export.
XLSWRITE will attempt to write file in CSV format.
> In xlswrite at 174
In readPlate>xlsExport_callback at 1035
Error using dialogCellstrHelper
Expected input to be one of these types:
char, cell
Instead its type was MException.
Error in dialogCellstrHelper (line 10)
validateattributes(inputStr, {'char','cell'}, {'2d'},mfilename);
Error in errordlg (line 45)
ErrorStringCell = dialogCellstrHelper(ErrorStringIn);
Error in readPlate/xlsExport_callback (line 1039)
errordlg(ME,'error');
Error while evaluating UIControl Callback
Jan (view profile)
great implementation, have been looking for something like this.
I am running growth curve analysis pretty frequently myself. Wishlist that would a lot of yeast people happy is:
1) integrated area under the curve (AUC) calculation by either trapezoid or Simpson's Rule method
2) variance or s.d. calculation of AUC using delta method, described in Gagnon and Peterson (1998)
Refael Ackermann (view profile)
Beautiful
Nitai Steinberg (view profile)
Please stay tuned for updates (suppose to be uploaded the next few days...)