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

FIATAS

:: 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

img2net

:: 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.

MicroCounter 1.00 – automatic Counting of Objects such as Bacterial Colonies from an JPEG Image

MicroCounter 1.00

:: DESCRIPTION

MicroCounter is a tool for automatic counting of objects such as bacterial colonies from an JPEG image. Typical usage is counting bacteria from a an image taken from a microscope.

::DEVELOPER

Leonid Asipov 

:: SCREENSHOTS

MicroCounter

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 MicroCounter

:: MORE INFORMATION

LSJuicer 0.2rc2 – Program for Squeezing Results from Linescan images

LSJuicer 0.2rc2

:: DESCRIPTION

LSJuicer is a multi-platform tool for analysing fluorescence vs. time data (e.g. linescan images from confocal microscopes, csv data from spectrophotometers, fluorimeters, etc)

::DEVELOPER

Laboratory of Systems Biology at Institute of Cybernetics

:: SCREENSHOTS

LSJuicer

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python
  • Java

:: DOWNLOAD

 LSJuicer

:: MORE INFORMATION

ImagePlane – Analysis of Images of the Animal S. Mediterranea

ImagePlane

:: DESCRIPTION

ImagePlane is python based image analysis software designed for the automated analysis of images of the animal S. mediterranea. This software allows the animals’s neoblasts to be quantified and tested for assymetries along its veritcal and hoizontal axes. ImagePlane also allows simple mophology categorizations to be made based on the overall shape of the animal.

::DEVELOPER

Yandell Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler
  • Python

:: DOWNLOAD

  ImagePlane

:: MORE INFORMATION

Image 3.10 – The Fingerprint Image Analysis system

Image 3.10

:: DESCRIPTION

Image is a package of analysis algorithms for processing gel images from restriction digest fingerprinting experiments.Image extracts a normalized band pattern for each lane (clone) on a gel. To achieve this several procedures are run on each gel in turn. The cycle starts when the user scans the film image or otherwise imports gel image data. The cycle ends when the normalized band position are transferred to a database and FPC takes over and matches up the clones to assemble contigs.

::DEVELOPER

Image Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Image

:: MORE INFORMATION

ParaCountStudio 3.1.0 – Count Cell Numbers within Image

ParaCountStudio 3.1.0

:: DESCRIPTION

ParaCountStudio is a program to count cell numbers within an image.ParaCountStudio has been developed to aid biologists needing to count large numbers of cells. It is a computer program written in Java that counts the number of cells that appear in an image, assuming a round cell shape and some degree of cell separation (ie. not tissues). The program has specifically been designed to distinguish red blood cells infected (or not) with malaria and stained with Giemsa, but the program is quite versatile and may work in a variety of other situations.

::DEVELOPER

Suzanne J Thomas. @ WEHI Bioinformatics

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

 ParaCountStudio

:: MORE INFORMATION