Time Lapse Analyser: Software Documentation

A tool for high throughput data processing for live cell imaging.

0. Introduction

This is the project homepage for the Time Lapse Analyser (TLA), a free, cross-platform, open source software for high throughput time-lapse data processing for live cell imaging. Currently we provide 21 different use cases, ranging from basic cell counting and image processing to wound healing assay analysis and cell tracking applications for differential interference contrast (DIC), phase contrast (PC), fluorescent imageing (FI) and brightfield microscopy images.

TLA is a graphical tool which enables easy access to high-throughput live cell imaging for every user, regardless of the individual expertise. Beginners can easily process stacks of time-lapse data by loading an apropriate image processing setup and time-lapse evaluation setup. Advanced users can modify existing setups, or create new setups which suit their need and special experimental conditions.

The online documentation provides a quick tour for beginners. Configuration files for predefined program setups are introduced in the setup section. The program and documentation are available in the download section. The source code is distributed under a Creative Commons Attribution-Noncommercial 3.0 License and available in section download.

1. Online Documentation

This software was designed to enable fast and easy access for new users. The basic user mode requires only a minimum amount of user interaction.

Running a time lapse analysis

Basic user mode screenshot
The upper graphic shows the basic user mode after opening the TLA. Only five steps are needed to run a predefined time-lapse analysis:
  1. Load avi file / set of avis
  2. Load setup file
  3. Choose saving directory
  4. Define file ending
  5. Start processing

Load avi file / set of avis

The first step is to load the set of time lapse files. This is done via the Open avis / set of avis menu entry or the Open Avi button. The avi files have to be either uncompressed or compressed with one of the following formats (Windows only): Indeo 3, Indeo 5, Cinepak, MSVC, RLE. The loaded files are visible in the drop-down list on the upper panel. Also the current active file can be changed there by selecting an item. During batch processing, the current processed file is shown in the drop down box as the current item as well as printed in the command window.

Load setup file

The next step is to load a predefined setup file. A setup file configures the image preprocessing operations and the time lapse analysis process. Some basic setups are described in section Setup, e.g. a multi-target-tracking on a set of cells. The advanced user mode (see Software documentation) provides a GUI to define additional setup settings.

Choose saving directory

The directory for file saving is set via the Browse button.

Define file ending

A unique file ending for the time lapse results can be set in the text field below the Browse button. All results are automatically saved under the avi file name extended by the user defined file ending. E.g. a list of avi files File1.avi, ..., File5.avi and the result ending _trackingresult will be saved after processing as File1_trackingresult.mat, ..., File5_trackingresult.mat.

Start processing

Before processing is started a valid saving directory and result file ending should be chosen. The default ending is "_trackingresult", the default saving directory is a folder "tlaresults" automatically created in the avi folder. Press "Start time lapse" and confirm the pixel sizes, magnification and recording time in the displayed dialog. After processing the TLA result viewer will open which provides some useful tools to display the tracking results, a video tool to superimpose the tracks into the avi file and some export functions.

Basic example

This section describes a step-by-step example on how to run a basic time lapse analysis setup configuration. This example setup is used for multi-target cell tracking in DIC (differential interference contrast) images. The mandatory cell confluence and image quality is shown by some example images which can be downloaded together with the setup file. Download the avi dic_panc1_vid1.avi as well as the sample setup setup_dic_tracking1.zip to follow this example.

Load avi file

Start the program and load the example1.avi file.
Basic user mode screenshot

The upper graphic shows the basic user mode after loading a video file. 

Load setup file

Unzip the setup_dic_tracking1.zip file and load the setup_dic_tracking1.mat file

Start processing

Before processing is started a valid saving directory and result file ending should be chosen. The default ending is _trackingresult, the default saving directory is a folder tlaresults automatically created in the avi folder. Press Start time lapse and confirm the pixel sizes, magnification and recording time in the following dialog. After the processing the result view will open in which the tracking results can be saved.
Basic user mode screenshot

3. Use cases and setup configuration

The advanced user mode gives access to various functions for image enhancing and video configuration. In this user mode a setup editor can be used to write own setup configurations.

Beneath basic use cases are given which illustrate the power of the setup editor. Each setup bundle includes at least sample images and a readme.txt file with detailed setup informations (Image resolution, recording technique, tested cell type, cell size, etc.).

Cell counting

Multi target cell tracking

Image stack processing

Video processing

Single Image processing

Proliferation analysis

Scratch wound assay analysis

Tube assay analysis

4. Installation

The software is written in MatLab and the files are compiled as a stand-alone Graphical User Interface (GUI) program. This software requires either a MatLab version (>=v. 7.2) or the MATLAB Compiler Runtime (MCR).
  1. Download the current Time Lapse Analyser version.
  2. Unzip the Time Lapse Analyser package.
  3. Install MCR If you do not have a Matlab version on your system. An MCRInstaller for each platform is included in the program's zip package.
  4. Start TimeLapseAnalyser by

Running the source code from within Matlab

If you are using the TLA-source code from within a Matlab environment, make sure to include all provided folders and subfolders into your Matlab path. This is most easily done using the genpath() function in combination with the addpath() function, e.g. addpath(genpath). If you want to add the paths permanently, use the function savepath() after you added the directories.

5. Download

Program
Windows 7 (32bit):
tla_win7_x86_v01_34.zip

Windows 7 (64bit):
tla_win7_x64_v01_34.zip

Windows XP (32bit):
tla_winXP_x86_v01_34.zip

Linux (64bit):
tla_linux_x64_v01_34.zip

Mac OSX Intel (64bit):
tla_mac_x64_v01_34.zip
Source
tla_src_v01_34.zip
Example videos
dic_panc1_vid1.avi (Example Video 1, DIC, Panc1 cells, migration)
dic_panc1_vid2.avi (Example Video 2, DIC, Panc1 cells, migration)
pc_hela_vid1.avi (Example Video 2, PC, HeLa cells, migration)
wound_panc1.AVI (Example Video 3, PC Panc1 cells, wound healing)
Documentation
Software Documentation (You need the Acrobat Reader to open the documentation.)
Version history
tla_src_v01_33.zip
tla_v01.29_src.zip
tla_v01.23_src.zip
tla_v01.22_src.zip

6. Misc

If you cannot open your avi video files with TimeLapseAnalyser, it may be due to an unsupported video codec (on Unix systems, avis must be uncompressed. On Windows systems supported codecs are: Cinepak, Indeo3, Indeo5, MSVC).
Also, avi files with special characters (like an '.' or '#' ) may not be readable by TLA.  
Under Windows, you can use virtualdub (http://www.virtualdub.org/) to decompress avi files.
Unfortunately, virtualdub is not working with Wine under Unix, but you can try out Avidemux (http://avidemux.org).  

If you experience problems with the TLA image processing results, check whether your Avis are compressed (if you are working on a windows machine). Strongly compressed avis may circumvent the image processing to work properly. If you have the possiblity to work with uncompressed material, make use of it. If only compressed material is available, the setup may have to be adjusted in the advanced user mode. 


Acknowledgements

Example Image and video file courtesy of:

7. License

TLA and TLA source code are licensed under a
Creative Commons License
This work is licensed under a Creative Commons Attribution-Noncommercial 3.0 License.


Contact/Imprint
Johannes Huth, Johann M. Kraus, Hans A. Kestler
last modified: 2010-11-16