FandPLimitTool
Parameter estimation problems play a central role in single molecule image analysis. Examples include determination of the 2D location of single molecules [1], estimating the level of defocus of single molecules [2] and [3], determining the distance of separation between two single molecules [4] and [5], estimation of photon count [6] etc. Common to all these problems is that it is helpful for the experimenter to have tools available that can quantify the accuracy with which various parameters can be estimated.
The FandPLimitTool is a GUI based software module that allows users to calculate the limits to the accuracy with which parameters can be estimated from single molecule imaging data. The software supports calculation of limits for the 2D/3D location estimation problem and the 2D/3D distance-estimation/resolution problem. The location estimation problem is concerned with the task of determining the position of a single molecule and the distance-estimation/resolution problem is concerned with the task of determining the distance of separation between two single molecules. The user can calculate limits for a variety of imaging scenarios.
The technical details of the methodology used for calculating the accuracy limits are given in [6]. The results of the location estimation problem are given in [1], [7] and [2]. The results for the resolution problem are given in [4] and [5].
The software is written in MATLAB and designed using the object oriented analysis and design methodology. The software has been designed to be extensible to allow for new models and numerical calculation routines.
References
[1] R. J. Ober, S. Ram, and E. S.Ward. Localization accuracy in single molecule microscopy. Biophysical Journal, 86:1185-1200, 2004.
[2] S. Ram, R. J. Ober, and E. S. Ward. How accurately can a single molecule be localized in three dimensions when imaged through a fluorescence microscope? Proc. of SPIE, 5699:426-435, 2005.
[3] S. Ram, J. Chao, P. Prabhat, E. S. Ward, and R. J. Ober. A novel approach to determining the three-dimensional location of microscopic objects with applications to 3D particle tracking. Proc. of SPIE, 6443:D1-D7, 2007.
[4] S. Ram, E. S. Ward, and R. J. Ober. Beyond Rayleigh's criterion: A resolution measure with application to single-molecule microscopy. PNAS, 103(12):4457-4462, 2006.
[5] S. Ram, A. V. Abraham, E. S. Ward, and R. J. Ober. A novel 3D resolution measure for optical microscopes with applications to single molecule imaging. Proc. of SPIE, 6444:6440-D9, 2007.
[6] S. Ram, E. S. Ward, and R. J. Ober. A stochastic analysis of performance limits for optical microscopes. Multidimensional Systems and Signal Processing, 17:27-57, 2006.
[7] S. Ram, E. S. Ward, and R. J. Ober. A novel resolution measure for optical microscopes: Stochastic analysis of the performance limits. Proceedings of the 2006 IEEE International Symposium on Biomedical Imaging, 770-773, 2006.
Version History
- V1.2 (June, 2012) This is the currently available version.
- V1.1 (May 8, 2008) Please note that this is a Beta version.
Minimum System Requirements
- PC with Pentium IV or equivalent processor suggested
- Windows XP Service Pack 2 *
- 256 MB RAM
- 1024 x 768 screen resolution
* Although MATLAB and the MCR are available on the Linux/Unix and MacOS platforms, this executable version of the software can run only on a PC with Windows XP and will NOT work in a Linux/Unix or Mac environment.
How to obtain the software
Please fill out and submit the Software User Information Form to request a copy of the Software. We will then send a reply to you with instructions for obtaining the software.
Download FandPLimitTool User’s Manual
Download FandPLimitTool Licence Agreement
FAQ
None available as yet.
Release Notes
The new version of FandPLimitTool (V1.2) provides several important features. First, the newly developed MUMDesignTool is incorporated with it and provides a user friendly framework to design the focal plane spacing for a MUM setup. Second, a new function called "Multivalue mode" is added to the software which allows the user to calaculate and plot the FIM for a range of different experimental parameters. Third, the FIM calculation codes are optimized which makes the software much faster than the previous version (i.e. V1.1).
Bug Reporting
We are constantly trying to improve this software and would be very grateful if you could send us a report on any bugs you find. Please send all bug reports to the email address wardlab@utsouthwestern.edu with the subject FandPLimitTool Bug. Please include as many details about the bug as you can, including details of all tasks that led up to exposure of the bug. This will help us in finding a solution to the problem. When we have a fix for the problem, we will release an updated version of the software. Please look in the Release Notes section for problems we are already aware of and have solutions for.
FandPLimitTool Development Team
- Raimund J. Ober (Team Leader)
- Sripad Ram
- Anish V. Abraham
- Amir Tahmasbi
- E. Sally Ward
Acknowledgements
The development work for FandPLimitTool was supported in part by the National Institutes of Health.
Contact Adress
Raimund J. Ober, Ph.D.
Professor
Adjunct Professor |
E. Sally Ward, Ph.D.
Professor |