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

FIATAS 1.0 – Fast Image AnnoTAtion Software

FIATAS 1.0

:: DESCRIPTION

FIATAS is used for assay annotation . The annotation tool has been developed with the idea that the editor/annotators are presented with the set of images associated with a single assay to be annotated, and an optimized anatomy ontology so the expert user can rapidly assign annotations to a given image set. Each image in the set can be independently annotated in terms of tissues/structures that show expression and the nature, strength and patterning of that expression. Comments can be added to any annotation as well as a general comment on the whole set.

::DEVELOPER

Eurexpress project

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

 FIATAS

:: MORE INFORMATION

img2net – Automated Network-based Analysis of Imaged Phenotypes

img2net

:: DESCRIPTION

Img2net is a software to automatedly analyze such structures by reconstructing the underlying network, computing relevant network properties, and statistically comparing networks of different types or under different conditions.

::DEVELOPER

Systems biology and Mathematical Modelling

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

 Img2net

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jul 26. pii: btu503.
img2net: automated network-based analysis of imaged phenotypes.
Breuer D, Nikoloski Z.

CRImage 1.34.0 – Tumour Image analysis

CRImage 1.34.0

:: DESCRIPTION

CRImage provides image analysis tools for segmentation, classification, and downstream analysis of tumour section images.

::DEVELOPER

the Markowetz lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R
  • BioConductor

:: DOWNLOAD

  CRImage

:: MORE INFORMATION

Citation

Quantitative image analysis of cellular heterogeneity in breast tumors complements genomic profiling
Y. Yuan, H. Failmezger, O.M. Rueda, H.R. Ali, S. Gräf, S-F. Chin, R.F. Schwarz, C Curtis, M.J. Dunning, H. Bardwell, N. Johnson, S. Doyle, G. Turashvili, E. Provenzano, S. Aparicio, C. Caldas, F. Markowetz
Science Translational Medicine, 4, 157ra142 (2012)

CFNet – Conic Convolution and DFT Network for classifying Microscopy Images

CFNet

:: DESCRIPTION

CFNet combines a novel rotation equivariant convolution scheme, called conic convolution, and the DFT to aid networks in learning rotation-invariant tasks. This network has been especially designed to improve performance of CNNs on automated computational tasks related to microscopy image analysis.

::DEVELOPER

Ma Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

CFNet

:: MORE INFORMATION

Citation

Bioinformatics. 2019 Jul 15;35(14):i530-i537. doi: 10.1093/bioinformatics/btz353.
Rotation equivariant and invariant neural networks for microscopy image analysis.
Chidester B, Zhou T, Do MN, Ma J.

SV-plaudit – Structural Variant Image Curation and Analysis

SV-plaudit

:: DESCRIPTION

SV-plaudit provides a pipeline for creating image views of genomic intervals, automatically storing them in the cloud, deploying a website to view/score them, and retrieving scores for analysis. SV-plaudit supports image generation sequencing data from BAM or CRAM files from Illumina paired-end sequencing, PacBio or Oxford Nanopore Technologies long-read sequencing, or 10X Genomics linked-read sequencing.

::DEVELOPER

The Quinlan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

SV-plaudit

:: MORE INFORMATION

Citation:

Gigascience. 2018 Jul 1;7(7). doi: 10.1093/gigascience/giy064.
SV-plaudit: A cloud-based framework for manually curating thousands of structural variants.
Belyeu JR et al.

CoGI – Towards Compressing Genomes as an Image

CoGI

:: DESCRIPTION

CoGI is a novel approach for genome compression, which transforms the genomic sequences to a two-dimensional binary image (or bitmap), then applies a rectangular partition coding algorithm to compress the binary image.

::DEVELOPER

The ADMIS group

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 CoGI

:: MORE INFORMATION

Citation

IEEE/ACM Trans Comput Biol Bioinform. 2015 Nov-Dec;12(6):1275-85. doi: 10.1109/TCBB.2015.2430331.
CoGI: Towards Compressing Genomes as an Image.
Xie X, Zhou S, Guan J.

CellX 1.12 – MATLAB Image Segmentation Package

CellX 1.12

:: 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.

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

:: 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.

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.