HDBIG – High Dimensional Brain Imaging Genomics

HDBIG

:: DESCRIPTION

HDBIG is a collection of software tools for high dimensional brain imaging genomics.

HDBIG-SR is an HDBIG toolkit focusing on Sparse Regression.

HDBIG-SCCA is an HDBIG toolkit focusing on Sparse Canonical Correlation Analysis (SCCA).

::DEVELOPER

ShenLab at Indiana University School of Medicine

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • MatLab

:: DOWNLOAD

 HDBIG-SR , HDBIG-SCCA

:: MORE INFORMATION

Citation

Yan J, Du L, Kim S, Risacher SL, Huang H, Moore JH, Saykin AJ, Shen L, for the ADNI (2014)
Transcriptome-guided amyloid imaging genetic analysis via a novel structured sparse learning algorithm.
Bioinformatics, Vol. 30 ECCB 2014, pages i564–i571.

Yan J, Huang H, Kim S, Moore JH, Saykin AJ, Shen L, for the ADNI (2014)
Joint identification of imaging and proteomics biomarkers of Alzheimer’s disease using network-guided sparse learning.
ISBI’14IEEE Int. Sym. on Biomedical Imaging, pp 665-668, Beijing, China, 28 April – 2 May, 2014.

ThunderSTORM 1.3 – ImageJ plugin for PALM and STORM data analysis and super-resolution imaging

ThunderSTORM 1.3

:: DESCRIPTION

ThunderSTORM is an open-source, interactive and modular plug-in for ImageJ designed for automated processing, analysis and visualization of data acquired by single-molecule localization microscopy methods such as photo-activated localization microscopy and stochastic optical reconstruction microscopy.

::DEVELOPER

Institute of Cellular Biology and PathologyFirst Faculty of MedicineCharles University in Prague, Czech Republic.

:: SCREENSHOTS

ThunderSTORM

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java
  • ImageJ

:: DOWNLOAD

 ThunderSTORM

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 25. pii: btu202. [Epub ahead of print]
ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging.
Ovesný M, Křížek P, Borkovec J, Svindrych Z, Hagen GM.

EXIMS 20141021 – EXploring Imaging Mass Spectrometry data

EXIMS 20141021

:: DESCRIPTION

EXIMS presents an improved data analysis pipeline based on a new peak picking method for EXploring Imaging Mass Spectrometry data.

::DEVELOPER

EXIMS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX / Window
  • MatLab

:: DOWNLOAD

 EXIMS

:: MORE INFORMATION

Citation

EXIMS: an improved data analysis pipeline based on a new peak picking method for EXploring Imaging Mass Spectrometry data.
Wijetunge CD, Saeed I, Boughton BA, Spraggins JM, Caprioli RM, Bacic A, Roessner U, Halgamuge SK.
Bioinformatics. 2015 Jun 10. pii: btv356.

Q-IHC 2 – Cancer Imaging Analysis tools

Q-IHC 2

:: DESCRIPTION

Q-IHC (Quantum IHC) is a set of cancer imaging analysis tools to assess Quantum Dots (QD) and Immunohistochemistry (IHC) based molecular and tissue images for various cancers types.

::DEVELOPER

Bio-MIBLab

:: SCREENSHOTS

Q-IHC

:: REQUIREMENTS

  • Windows
  • MatLab

:: DOWNLOAD

 Q-IHC

:: MORE INFORMATION

Citation:

Xing Y, Chaudry Q, Shen C, Kong KY, Zhau HE, Chung LW, Petros JA, O.Regan RM, Yezhelyev MV, Simons JW, *Wang MD, and *Nie SM
Bioconjugated quantum dots for multiplexed and quantitative immunohistochemistry.
Nat Protoc. 2007 May 3; 2(5):1152-65.

pLSA – Probabilistic Latent Semantic Analysis of Imaging Mass Spectrometry Data

pLSA

:: DESCRIPTION

pLSA contains MATLAB code to perform a probabilistic Latent Semantic Analysis of Imaging Mass Spectrometry Data. In contrast to other unsupervised methods like Principal Component Analysis or Independent Component Analysis this method accounts for the non-negativity of mass spectra.

::DEVELOPER

Hamprecht lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • MatLab

:: DOWNLOAD

 pLSA

:: MORE INFORMATION

Citation

Anal Chem. 2008 Dec 15;80(24):9649-58. doi: 10.1021/ac801303x.
Concise representation of mass spectrometry images by probabilistic latent semantic analysis.
Hanselmann M1, Kirchner M, Renard BY, Amstalden ER, Glunde K, Heeren RM, Hamprecht FA.

RootArray – Microfluidic Device for Automated High Throughput Live Imaging of Gene Expression

RootArray

:: DESCRIPTION

RootArray is an imaging pipeline that includes automated tracking of growing roots, automated image acquisition and gene expression quantification.

::DEVELOPER

Uwe Ohler’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • C++ Compiler / Java

:: DOWNLOAD

 RootArray

:: MORE INFORMATION

SIA 0.9.0.23 – Shotgun Imaging software

SIA 0.9.0.23

:: DESCRIPTION

SIA (Shotgun Imaging Analyzer) is a shotgun imaging software to allow visual assessment of the proteomic profiles along biopsies or surfaces.

::DEVELOPER

Laboratory for Proteomics and Protein Engineering

:: SCREENSHOTS

SIA

:: REQUIREMENTS

  • Windows
  • .NET Framework 4.5
  • SQL Server

:: DOWNLOAD

 SIA

:: MORE INFORMATION

Citation

J Proteome Res. 2014 Jan 3;13(1):314-20. doi: 10.1021/pr400919k. Epub 2013 Nov 27.
Exploring the proteomic landscape of a gastric cancer biopsy with the shotgun imaging analyzer.
Aquino PF1, Lima DB, de Saldanha da Gama Fischer J, Melani RD, Nogueira FC, Chalub SR, Soares ER, Barbosa VC, Domont GB, Carvalho PC.

Micropilot v094 – Automation of Fluorescence Microscopy–based imaging

Micropilot v094

:: DESCRIPTION

The Micropilot software from EMBL is a computer program that can rapidly learn what a scientist is looking for in an experiment and then take over the laborious and time-consuming task, automatically performing complex microscopy experiments when it detects cells with interesting features.

::DEVELOPER

Advanced Light Microscopy Facility,EMBL

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Micropilot

:: MORE INFORMATION

Citation

Christian Conrad et al.
Micropilot: automation of fluorescence microscopy–based imaging for systems biology
Nature Methods 8, 246–249 (2011) doi:10.1038/nmeth.1558