SLIF 2-2 – Subcellular Location Image Finder

SLIF 2-2

:: DESCRIPTION

SLIF finds fluorescence microscope images in on-line journal articles, and indexes them according to cell line, proteins visualized, and resolution.

::DEVELOPER

Murphy Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Matlab
  • Java

:: DOWNLOAD

 SLIF

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Feb 15;24(4):569-76.
Improved recognition of figures containing fluorescence microscope images in online journal articles using graphical models.
Qian Y, Murphy RF.

FLINO – ImmunoFLuorescence Image NOrmalization

FLINO

:: DESCRIPTION

FLINO repository provides R-scripts and data to perform and evaluate image normalizations methods and workflows.

::DEVELOPER

FLINO team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R
:: DOWNLOAD

FLINO

:: MORE INFORMATION

Citation

Graf J, Cho S, McDonough E, Corwin A, Sood A, Lindner A, Salvucci M, Stachtea X, Van Schaeybroeck S, Dunne PD, Laurent-Puig P, Longley D, Prehn JHM, Ginty F.
FLINO-A new method for immunofluorescence bioimage normalization.
Bioinformatics. 2021 Oct 2:btab686. doi: 10.1093/bioinformatics/btab686. Epub ahead of print. PMID: 34601553.

SCIP 1.0 – Single-Cell Image Processor

SCIP 1.0

:: DESCRIPTION

SCIP is an open source multi-channel, multi-process, time-lapse morphological and functional microscopy images analyser.

::DEVELOPER

Andre Ribeiro’s Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux/ MacOsX
  • MatLab

:: DOWNLOAD

SCIP

:: MORE INFORMATION

Citation:

Martins L, Neeli-Venkata R, Oliveira SMD, Häkkinen A, Ribeiro AS, Fonseca JM.
SCIP: a single-cell image processor toolbox.
Bioinformatics. 2018 Dec 15;34(24):4318-4320. doi: 10.1093/bioinformatics/bty505. PMID: 29931314.

HTML5 PivotViewer 1.0 – A HTML5 Data Exploration Tool for Image based data sets

HTML5 PivotViewer 1.0

:: DESCRIPTION

HTML5 PivotViewer is a novel, open source, platform-independent viewer making use of the latest web technologies that allows seamless access to images and associated metadata for each image.

::DEVELOPER

The Computational Biology Research Group (CBRG)

:: SCREENSHOTS

PivotViewer

:: REQUIREMENTS

  • HTML5 Web Browser

:: DOWNLOAD

 HTML5 PivotViewer

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 May 21. pii: btu349. [Epub ahead of print]
HTML5 PivotViewer: High throughput visualisation and querying of image data on the web.
Taylor S1, Noble R2.

Frida 1.1.0 – FRamework for Image Dataset Analysis

Frida 1.1.0

:: DESCRIPTION

Frida (FRamework for Image Dataset Analysis) is image analysis software. Frida was developed by the Johns Hopkins University Tissue Microarray Core Facility. Frida is open source and written in 100% Java. Frida makes use of functionality from the NIH’s ImageJ application.

::DEVELOPER

JHU Tissue MicroArray Core Facility

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • Java

:: DOWNLOAD

Frida

:: MORE INFORMATION

Citation:

Cornish T, Morgan J, Gurel B, and De Marzo AM.
FrIDA: An open source framework for image dataset analysis.
Arch. Pathol. Lab. Med. 132:856 (2008). Originally presented at Advancing Practice, Instruction and Innovation Through Informatics: Pittsburgh, PA, 2007.

TiltPicker 2.0b13 – Particle Picker for Image Tilt Pairs

TiltPicker 2.0b13

:: DESCRIPTION

TiltPicker is a graphical user interface for picking particles from image tilt pairs for such applications as random conical tilt (RCT) and orthogonal tilt reconstruction (OTR).

::DEVELOPER

The National Resource for Automated Molecular Microscopy (NRAMM)

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / WIndows / MacOsX
  • Python

:: DOWNLOAD

TiltPicker

:: MORE INFORMATION

Citation:

Voss NR, Yoshioka CK, Radermacher M, Potter CS, Carragher B. (2009)
DoG Picker and TiltPicker: software tools to facilitate particle selection in single particle electron microscopy.
J Struct Biol. v166(2): pp. 205-13.

BRIG 0.95 – BLAST Ring Image Generator

BRIG 0.95

:: DESCRIPTION

BRIG is a cross-platform application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data.

::DEVELOPER

Beatson Microbial Genomics Lab.

:: SCREENSHOTS

brig

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 BRIG

:: MORE INFORMATION

Citation

BMC Genomics. 2011 Aug 8;12:402. doi: 10.1186/1471-2164-12-402.
BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons.
Alikhan NF1, Petty NK, Ben Zakour NL, Beatson SA.

MCF – Image Segmentation Algorithms for automated Single Cell Analysis

MCF

:: DESCRIPTION

The MCF (Model Controlled Flooding) image segmentation algorithms and example code for automated single cell analysis.

::DEVELOPER

Mike West

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Matlab

:: DOWNLOAD

 MCF

:: MORE INFORMATION

Citation

Model-controlled flooding with applications to image reconstruction and segmentation.
Wang Q, West M.
J Electron Imaging. 2012 Jun 22;21(2). doi:pii: 023020.

CellX 2.12 – MATLAB Image Segmentation Package

CellX 2.12

:: DESCRIPTION

CellX is a tool for segmentation, fluorescence quantification, and tracking of cells on microscopy images.

::DEVELOPER

CSB – Computational Systems Biology Group

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows/Linux/MacOsX
  • MatLab

:: DOWNLOAD

 CellX

:: MORE INFORMATION

Citation

Using CellX to quantify intracellular events.
Mayer C, Dimopoulos S, Rudolf F, Stelling J.
Curr Protoc Mol Biol. 2013;Chapter 14:Unit 14.22.. doi: 10.1002/0471142727.mb1422s101.

Bioinformatics. 2014 Sep 15;30(18):2644-51. doi: 10.1093/bioinformatics/btu302. Epub 2014 May 21.
Accurate cell segmentation in microscopy images using membrane patterns.
Dimopoulos S, Mayer CE, Rudolf F, Stelling J.

IMAGE 2.4.1 – Iterative Mapping and Assembly for Gap Elimination

IMAGE 2.4.1

:: DESCRIPTION

IMAGE ( Iterative Mapping and Assembly for Gap Elimination) is a software designed to close gaps in any draft assembly using Illumina paired end reads. IMAGE is best described in several stages: aligning of Illumina reads at contig ends; local assembly of reads into new contigs; reference contigs are extended or merged; iterating the whole process to extend and merge more contigs.

::DEVELOPER

IMAGE team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 IMAGE

:: MORE INFORMATION

Citation

Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps.
Tsai IJ, Otto TD and Berriman M
Genome biology 2010;11;4;R41