Farsight 0.4.4 – Quantitative Tools for Studying Complex and Dynamic Biological Microenvironments from 4D/5D Microscopy Data

Farsight 0.4.4

:: DESCRIPTION

The goal of the FARSIGHT project is to develop and disseminate a next-generation toolkit of image analysis methods to enable quantitative studies of complex & dynamic tissue microenvironments that are imaged by modern optical microscopes. Examples of such microenvironments include brain tissue, stem cell niches, developing embryonic tissue, immune system components, and tumors. Progress in mapping these microenvironments is much too slow compared to the need. Our knowledge of these systems has been painstakingly “pieced together” from large numbers of fixed, 2-D images of specimens revealing a small fraction of the molecular ‘players’ involved. The goal of this project is to help accelerate progress by: (i) harnessing the power of modern microscopy to help see the microenvironments in a much more detailed, direct, and comprehensive manner; and (ii) computational tools to analyze the multi-dimensional data produced by these microscopes.

::DEVELOPER

Farsight Team

:: SCREENSHOTS

:: REQUIREMENTS

Windows / MacOSX /Linux

:: DOWNLOAD

Farsight

:: MORE INFORMATION

Citaition

The FARSIGHT trace editor: an open source tool for 3-D inspection and efficient pattern analysis aided editing of automated neuronal reconstructions.
Luisi J, Narayanaswamy A, Galbreath Z, Roysam B.
Neuroinformatics. 2011 Sep;9(2-3):305-15. doi: 10.1007/s12021-011-9115-0.

qPCR-DAMS 1.2 – Analyze, Manage, and Store Quantitative Real-Time PCR data.

qPCR-DAMS 1.2

:: DESCRIPTION

qPCR-DAMS is a database management system implemented on MS Access 2003 and Visual Basic. It is designed to analyze, manage, and store relative and absolute quantitative real-time PCR data. The system consists of 5 blocks: three blocks (Gene, Plate, and Experiment) for inputting, storing and describing raw data, and two blocks (View data and Process Data) for checking, evaluating, and processing data. Users are allowed to choose among four basic outputs: (I) Ratio relative quantification, (II) Absolute level, (III) Normalized absolute expression, and (IV) Ratio absolute quantification, and two advanced options: (V) Multiple reference relative quantification and (VI) Multiple references absolute quantification, within single software package. The coefficient of variation is monitored at each step during data processing and the accuracy is further improved by an easy data tracking and display system. In summary, qPCR-DAMS is a handy novel tool for real-time PCR users.

::DEVELOPER

Nili Jin , Keyu He and Lin Liu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows
Microsoft Access 2000 or above

:: DOWNLOAD

qPCR-DAMS

:: MORE INFORMATION

Citation

Nili Jin , Keyu He and Lin Liu
qPCR-DAMS: a database tool to analyze, manage, and store both relative and absolute quantitative real-time PCR data
Physiological Genomics 25:525-527 (2006)

DART-PCR 1.0 – Quantitative Real-time PCR Data Analysis

DART-PCR 1.0

:: DESCRIPTION

DART-PCR (Data Analysis for Real‐Time PCR) provides a simple means of analysing real-time PCR data from raw flurescence data. This allows an automatic calculation of amplification kinetics, as well as performing the subsequent calculations for relative quantification and calculation of assay variability. Amplification efficiencies are also tested to dtect anomalus samples within groups (outlayers) and differences between experimatal groups (amplification equivalence).

::DEVELOPER

Stuart N. Peirson, Jason N. Butler and Russell G. Foster

:: SCREENSHOTS

:: REQUIREMENTS

Excel

:: DOWNLOAD

DART-PCR

:: MORE INFORMATION

Citation

Stuart N. Peirson, Jason N. Butler and Russell G. Foster (2003)
Experimental validation of novel and conventional approaches to quantitative real-time PCR data analysis
Nucl. Acids Res. (2003) 31 (14): e73

DCellIQ 1.0 – Quantitative Time-lapse Nuclei Image Analysis

DCellIQ 1.0

:: DESCRIPTION

DCellIQ ( Dynamic Cell Image Quantitator ) is a user-friendly software package that is designed for quantitative time-lapse nuclei image analysis for cell cycle studies, whose key features include automated nuclei detection, segmentation, quantification, tracking, cell cycle phase identification, and statistical analysis of the cell cycle duration.

::DEVELOPER

TMHRI Center for Bioengineering and Informatics

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / Mac OsX
MATLAB

:: DOWNLOAD

DCellIQ

:: MORE INFORMATION

NeuriteIQ 1.0 – Quantitative Neurite Image Analysis

NeuriteIQ 1.0

:: DESCRIPTION

NeuriteIQ ( Neurite Image Quantitator ) is a user-friendly software package that is designed for quantitative Neurite image analysis, whose key features include automated neurite labeling and quantification of their length and brightness.

::DEVELOPER

TMHRI Center for Bioengineering and Informatics

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / Mac OsX
MATLAB

:: DOWNLOAD

NeuriteIQ

:: MORE INFORMATION

Citation:

Y. Zhang, X. Zhou, A. Degterev, M. Lipinski, D. Adjeroh, J. Yuan, and S.T. Wong,
Automated neurite extraction using dynamic programming for high-throughput screening of neuron-based assays,
NeuroImage, Vol. 35, issue 1, pp. 1502-15, Sept. 2007

NeuronIQ 1.5 – Quantitative Neuron Image Analysis

NeuronIQ 1.5

:: DESCRIPTION

NeuronIQ ( Neuron Image Quantitator ) is a user-friendly software package that is designed for quantitative Neuron image analysis, whose key features include automated dendrite and spine detection, quantification, and spine phenotype classification.

::DEVELOPER

TMHRI Center for Bioengineering and Informatics

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / Mac OsX
MATLAB

:: DOWNLOAD

NeuronIQ

:: MORE INFORMATION

Citation:

J. Cheng, X. Zhou, E. Miller, R.M. Witt, J. Zhu, B.L.Sabatini and S.T. Wong,
A novel computational approach for automatic dendrite spines detection in two-photon laser scan microscopy,
Journal of Neuroscience Method, 165(1):122-134, Sept. 2007

ZFIQ 1.0 – Quantitative Zebrafish Image Analysis

ZFIQ 1.0

:: DESCRIPTION

ZFIQ ( Zebrafish Image Quantitator ) is a user-friendly software package that is designed for quantitative Zebrafish image analysis, whose key features include automated cell detection, segmentation, quantification, and phenotype classification.

::DEVELOPER

TMHRI Center for Bioengineering and Informatics

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

ZFIQ

:: MORE INFORMATION

Citation:

Tianming Liu.
A quantitative zebrafish phenotyping tool for developmental biology and disease modeling.
IEEE Signal and Processing Magazine. 24(1):126-129. 2007

BQGB 090528 – Berkeley Quantitative Genome Browser

BQGB 090528

:: DESCRIPTION

BQGB (Berkeley Quantitative Genome Browser, sometimes known as “bbrowse”, “bbrowser”) duplicates much of the annotation display functionality typical of a genome browser but with an emphasis on custom and quantitative data such as that produced in high throughput sequencing and genome-wide association studies. The application runs locally on a user’s desktop or laptop computer, avoiding the slow back-and-forth of web based genome browsers. BQGB expects data files to be local to the application process and in a file format such as GFF, BED, SGR, WIG, FASTA or any column delimited format that provides sequence and base pair position locations. This topography should generally be faster than that of a central remote database plus web based browser when working with many custom files, ie. downloading a single reference annotation to one’s local machine is quicker than uploading hundreds of custom data files to a remote server!

::DEVELOPER

Berkeley Drosophila Transcription Network Project

:: SCREENSHOTS

:: REQUIREMENTS

Windows / MacOsX / Linux
QT
GCC

:: DOWNLOAD

BQGB

:: MORE INFORMATION

License