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Presenting iSMS: single-molecule FRET microscopy software

posted 30 Jun 2015, 16:44 by Søren Preus   [ updated 30 Jun 2015, 16:59 ]

If you are interested in single-molecule FRET you may find our new freeware iSMS useful. iSMS is published in the 2015 july issue of Nature Methods.

iSMS provides a comprehensive, user-interfaced platform for analysing raw and processed video data from single-molecule FRET TIRF microscopy using immobilized molecules. The website includes demo data and the software is particularly useful for newly started groups and beginners to intermediate smFRET users.

iSMS main window

Motivation

While smFRET has been around for more than 15 years analysing smFRET data is still a cumbersome and tedious task requiring user-intervention at several critical steps. In particular, the choices made by the investigator, knowingly or unknowingly, during the smFRET data analysis can make it difficult to compare data obtained from different labs quantitatively. We have tried to address this issue by developing a more transparent analysis workflow and easy sharing of both raw and processed smFRET data. In the end we hope to standardize smFRET data analysis across different labs allowing peers, PI's and collaborators to explore and evaluate smFRET data more easily.

Have a great summer,
Søren Preus - FluorTools.com

a|e updated to 2.2

posted 26 Jan 2015, 08:15 by Søren Preus   [ updated 26 Jan 2015, 08:20 ]

The UV-Vis spectral analysis software a|e has been updated to version 2.2. This new version includes a number of bug fixes and improved compatibility with newer versions of MATLAB.

The number of developers is now doubled

I am particularly happy to have Daniel Aron Gudnason from Aarhus University, Denmark, as a co-developer on this version. Daniel is a talented PhD fellow in optical spectroscopy who will take part in developing the future versions of a|e. Daniel here tells about a new amendment he made for quickly plotting spectral trends over a range of data sets:

Plot trends in multiple data sets

With this new version of a|e a new module, called the “Extracted Value Plotter”, has been added. The modules grants the user the following functionalities: 

  • The ability to plot data points extracted within the program – e.g. single value wavelength intensities or integrated intensities
  • The ability to plot these extracted values for different sets of spectra as data series in the same graph
  • User defined x-values to plot against (time, etc.)
  • Export of the figure for final editing and to be saved in formats supported for matlab figures 
In future releases the following functionalities will be added to the module
  • A general purpose fit tool to fit the data 
  • A way to manipulate with the extracted data series, i.e. arithmetic manipulation 
  • A more integrated way of exporting figures with extra features such as transparent background 
  • More features to customize the produced graphs 
To activate the new feature, navigate to the menu Tools->Plot trends. Once activated, the values obtained when integrating multiple selected spectra or from extracting wavelength values using 'Tools->Data extraction', can be plotted in the trend window located at 'Tools->Plot trends->Open trend window'.


You can develop new functionalities for a|e

Note that you are free to customize the program yourself. Daniel used source files from the MATLAB version of a|e to get acquainted with the program structure before writing the new module. Drop me an email if you too are interested in sharing your developments with other users.


Have a great day!

Søren Preus, FluorTools.com

a|e updated to 2.1

posted 15 Apr 2014, 17:37 by Søren Preus   [ updated 15 Apr 2014, 17:39 ]

The spectral analysis software a|e has been updated to version 2.1. The new version has some new tools but mainly fixes a number of minor bugs introduced with version 2.0.

Import spectra from online databases

It is now possible to import spectra directly from URL links. An example is shown here:

1. Go to an online database, such as fluorophore.org.

2. Pick your dye and select the Spectra tab. Then, right-click the download link and select "Copy link".


3. Go to a|e -> File -> Load data -> Import from URL (or press Ctrl+U)


4. Insert the link address and press OK.


5. The data at the URL is added as new files in the software.


Best,
Søren

a|e upgraded to 2.0

posted 31 Mar 2014, 15:04 by Søren Preus   [ updated 1 Apr 2014, 11:39 ]

The UV-Vis-IR spectral analysis software a|e has received a considerable facelift and several new tools and improvements have been added.


Fundamental changes

  • First of all, the GUI and program structure has been trimmed to allow new features and extensions to be more easily implemented. This includes a default settings structure and a smart-resizable GUI window. Many tools has been moved to new figure windows and popup info-boxes are now integrated into the software.
  • The new default colors of the graph window is white axes on a black background. This can easily be changed back to black on white background from the View->Plot properties menu. Exported figures are always on a white background.
  • The compiled program is packed into a single installation file. The setup automatically checks if the required MATLAB Compiler Runtime environment is installed on the target computer. If the MCR is missing, it will be downloaded and installed automatically. The new slick splash screen looks like this:


New functionalities include:

  • One-click copy of graph to the clipboard. This addition greatly increases the speed of creating figures for Power Point presentation, Microsoft Word updates, etc.. The properties of the exported figure, such as its size and linewidths, can be customized from the (new) settings menu.
  • A new spectral library of >300 dyes is implemented directly in the software. Currently, dye spectra from ATTO-Tec and Life Technologies have been included. The library is convenient for finding dyes based on their spectral properties.
  • Copy data points to clipboard. The data can then be pasted into cell sheets in e.g. Origin Pro or Excel for further analysis.
  • Import and export to/from Excel.
  • A 'recent files' menu has been added.
  • The plot window is now more customizable: Set default graph linewidths, linetypes, background color, etc.
  • The data list can be grouped by colorizing listbox items.
  • ...and more


Usage statistics

The program now collects usage statistics - if the user chooses to allow this setting in the Help menu. Usage stats are 100% anonymous and does not give away any personal or data-related information. All it does is register the number of times a given tool has been used and uploads this count number to a server upon closing the software. Usage stats provides the developer, me, with insight into where there is room for improvement.

Impact of a|e 1.2

The previous version 1.2 reached close to 250 downloads per month with the 3 most active countries being the Unites States, India and Germany.

a|e was recently cited in JACS in which the spectral decomposition algorithm was used to fit spectra of mixed polymer-fullerene species.

With the new amendments I can more easily build on the software in the future. Let me know if you have any particular needs or suggestions.

All the best,
Søren

AniFit updated to version 1.3

posted 22 Oct 2013, 04:34 by Søren Preus   [ updated 22 Oct 2013, 04:35 ]

The fluorescence anisotropy decay analysis software, AniFit, has been upgraded to version 1.3. This version introduces a lot of changes "behind the scene" while the main features of the GUI are the same. 


The reason for most of the changes is that I am working towards a more general and transparent code of the software on the site that will share the same principles and functions throughout different programs. This should make it easier in the future for people interested in modifying the software for their own needs, as well as for me to update the software and implement new functionalities.


New functionalities:

  • There is a new "Developers menu" in the Help menu of the MATLAB version for people interested in editing the program. This can be used to get insight into GUI, data and settings structures etc.. I will post more information on this topic in the future.
  • Plot r(t) only starting from "time zero". Thanks to Mélina Gilbert and Damir Dzebo, Chalmers University, for the suggestion. Time zero is currently defined as the peak of the IRF minus 1 channel.
  • Plot r(t) as either dotted or full-drawn line (default is dotted).
  • Plot r(t) with/without IRF.
  • Modify/change the default program settings.
  • Load/save settings from file.
  • Export data and fits to MATLAB workspace (only MATLAB version).
  • Direct link to the Bug report from the Help menu.
  • Checks for updates on start-up, or at will.

Improvements to existing functionalities:

  • Faster calculation of chi-square surfaces.
  • Faster plot updating.

Bug fixes:

  • Several minor bug fixes and code improvements in general.
  • Fixed bug when trying to fit decay times close to 0 ns.
  • Fixed bug when running chi-square surfaces with scatter included.

The look and feel:

  • Some menus are rearranged.
  • The GUI icon has been changed.
  • The new splash screen looks like this:


FluorFit updated to version 1.3 and is now called DecayFit

posted 11 Sep 2013, 18:20 by Søren Preus   [ updated 11 Sep 2013, 19:18 ]

In agreement with PicoQuant GmbH (Berlin, Germany), FluorFit has been renamed to DecayFit to avoid confusion with the commercially available FluoFit. 

DecayFit and FluoFit are both fluorescence decay analysis software that has many of the same functionalities and the choice of FluorFit did not warrant a clear distinction between the two. DecayFit is released under the GNU General Public License and therefore does not offer any warranty or guarantee what so ever. FluoFit is a professional counterpart.


New in version 1.3

Aside from the new name, a number of improvements have been added to the software:

- The program now automatically identifies time and intensity columns in data files. There is thus no longer any need to format the input data in any particular way.
- A data import wizard can be forced if automated import failed.
- Two or more data sets can be merged/summed. This is convenient if the same sample has been measured using two or more acquisitions.
- Loading/saving sessions remembers last opened/saved file.
- Fixed bug when setting ns/channel.
- Fixed bug in delete function.

- The software now automatically checks for new updates. See my related MATLAB-tutorial on how to implement automated updating in MATLAB.


a|e updated to version 1.2

posted 3 Sep 2013, 11:32 by Søren Preus   [ updated 4 Sep 2013, 01:29 ]

This version is not just an update but also an upgrade. New functions are implemented in the software whenever I'm in a need of these functionalities myself, or when people ask for them. Version 1.2 has a number of new practical functionalities implemented. 

New functionalities:

 - Import data directly from Origin project (OriginLab Corp.). This function exploits my first contribution to the MATLAB File Exchange: importOrigin
 - Support for IR spectra: Transmittance <-> Absorbance. Label peaks. Thanks to Amin from Sharif University, Iran, for inducing the idea.
 - Merge sessions.
 - Subtract minimum value from spectrum.
 - Plot the original spectrum when a fitted spectrum is selected.
 - The program now checks for new updates when loading the GUI.

Improvements to existing functionalities:

 - Straight-line fit is more robust.
 - Improved algorithm for decomposing spectra.
 - Loading/saving tools remembers last saved/opened file.
 - Added an integration menu tool for specifying all spectra and wavelengths.
 - Added a normalization menu defining a range of spectra to normalize and their normalization wavelength.
 - Trimmed the toolbar.
   

Bug fixes: 

 - Fixed bug when calculating spectral overlap integrals using spectra with <0.5 nm grid spacing. Thanks to Thangaraju from Paris, France, for reporting the bug.
 

Welcome to the announcement page

posted 21 Aug 2013, 04:55 by Søren Preus   [ updated 10 Sep 2013, 01:30 ]

A big welcome to the announcement page. Its purpose is to provide a means to stay tuned with the latest versions of the software from this site. By subscribing to the email service and/or RSS feed you will get notified when new posts are made. I sincerely hope I will find the time to post here regularly.

Stats from the first months of FluorTools.com

I decided to make a subscribableblebl (?) announcement page because the stats of the site has increased steadily since its launch in late 2012/early 2013. Here are the first modest, but motivating, stats of the site.

Downloads of current software versions

a|e 1.1: 221 downloads since June 19th (110 downloads/month)

DecayFit 1.2: 82 downloads since June 27th (45 downloads/month)

AniFit 1.2/1.1c: 20 downloads since July 1st (12 downloads/month)

FRETmatrix 1.1: 91 downloads since Nov 14th (10 downloads/month)

Site visits

Monthly site visits (January-July):


Daily visits the past month (21/7-20/8):

Total per month: 1403 visits (1066 unique visitors)

The five most visited pages:

1-8 of 8