LeafNet 0.0.1 – A CNN for Plant Identification

LeafNet 0.0.1

:: DESCRIPTION

LeafNet is a method based on a convolutional neural network (CNN) to identify plants from images of leaves.

::DEVELOPER

BioInfWeb projects

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

LeafNet

:: MORE INFORMATION

Citation

LeafNet: A computer vision system for automatic plant species identification
Author links open overlay panelPierreBarréaBen C.StöverbKai F.MüllerbVolkerSteinhagea
Ecological Informatics Volume 40, July 2017, Pages 50-56

ImageJ 2.0.0 rc71 – Image Processing & Analysis in Java

ImageJ 2.0.0 rc71

:: DESCRIPTION

ImageJ is a public domain Java image processing program.ImageJ was designed with an open architecture that provides extensibility via Java plugins and recordable macros. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems.

::DEVELOPER

ImageJ team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

ImageJ

:: MORE INFORMATION

Citation:

Abramoff, M.D., Magelhaes, P.J., Ram, S.J. “Image Processing with ImageJ“.
Biophotonics International, volume 11, issue 7, pp. 36-42, 2004.

YeastSpotter 2.1 – Yeast Segmentation Web Tool

YeastSpotter 2.1

:: DESCRIPTION

YeastSpotter is a web application for the segmentation of yeast microscopy images into single cells. YeastSpotter is user-friendly and generalizable, reducing the computational expertise required for this critical preprocessing step in many image analysis pipelines.

::DEVELOPER

Alan Moses’ Computational Biology Lab,University of Toronto

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

YeastSpotter

:: MORE INFORMATION

Citation

Bioinformatics. 2019 Nov 1;35(21):4525-4527. doi: 10.1093/bioinformatics/btz402.
YeastSpotter: accurate and parameter-free web segmentation for microscopy images of yeast cells.
Lu AX, Zarin T, Hsu IS, Moses AM

CRImage 1.30.0 – Tumour Image analysis

CRImage 1.30.0

:: 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)

KymoRod 0.10.0 – Matlab Graphical Interface for the Study of Hypocotyl Growth

KymoRod 0.10.0

:: DESCRIPTION

KymoRod is a method for automated kinematic analysis of rod-shaped plant organs.

::DEVELOPER

IJPB Modeling and digital imaging lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • MatLab

:: DOWNLOAD

 KymoRod

:: MORE INFORMATION

Citation

KymoRod: A method for automated kinematic analysis of rod-shaped plant organs.
Bastien R, Legland D, Martin M, Fregosi L, Peaucelle A, Douady S, Moulia B, Höfte H.
Plant J. 2016 Jun 29. doi: 10.1111/tpj.13255.

MorphoLibJ 1.2.2 – Collection of Mathematical Morphology Methods and Plugins for ImageJ

MorphoLibJ 1.2.2

:: DESCRIPTION

The MorphoLibJ library proposes a large collection of generic tools based on mathematical morphology to process binary and grey-level 2D and 3D images, integrated into user-friendly plugins.

::DEVELOPER

IJPB Modeling and digital imaging lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java
  • ImageJ

:: DOWNLOAD

 MorphoLibJ

:: MORE INFORMATION

Citation

MorphoLibJ: integrated library and plugins for mathematical morphology with ImageJ.
Legland D, Arganda-Carreras I, Andrey P.
Bioinformatics. 2016 Jul 13. pii: btw413.

LEVER – Stem Cell Segmentation, Tracking and Lineaging

LEVER

:: DESCRIPTION

LEVER (Lineage Editing and Validation) is a collection of software tools for analyzing the development of proliferating (dividing) cells in time-lapse microscopy image sequences. LEVER includes algorithms for segmentation, tracking and lineaging. LEVER also includes a user interface that allows the segmentation, tracking and lineaging results to be validated, with any errors in the automated processing easily identified and quickly corrected

CloneView is an incredibly useful tool for visualizing the results from the LEVER program together with the image data.

::DEVELOPER

computational image sequence analysis

:: SCREENSHOTS

LEVER

:: REQUIREMENTS

  • Windows
  • MatLab

:: DOWNLOAD

 LEVER

:: MORE INFORMATION

Citation

LEVER: software tools for segmentation, tracking and lineaging of proliferating cells.
Winter M, Mankowski W, Wait E, Temple S, Cohen AR.
Bioinformatics. 2016 Jul 16. pii: btw406.

Imaris 8.3 – Analysis, Segmentation and Interpretation of 3D and 4D Microscopy datasets

Imaris 8.3

:: DESCRIPTION

Imaris is Bitplane’s core scientific software module for data visualization, analysis, segmentation and interpretation of 3D and 4D microscopy datasets.

::DEVELOPER

BITPLANE AG

:: SCREENSHOTS

Imaris

:: REQUIREMENTS

  • Windows/MacOsX

:: DOWNLOAD

 Imaris

:: MORE INFORMATION

3DEM Loupe – Normal Mode Analysis (NMA) of Electron Microscopy (EM) volumes

3DEM Loupe

:: DESCRIPTION

3DEM Loupe allows Normal Mode Analysis (NMA) of Electron Microscopy (EM) volumes . Results can be fully explored in 3D through animations and movies generated by the server, and special care has been given to a user-friendly interface

::DEVELOPER

Biocomputing Unit – CNB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

3DEM Loupe: Analysis of macromolecular dynamics using structures from electron microscopy.
Nogales-Cadenas R, Jonic S, Tama F, Arteni AA, Tabas-Madrid D, Vázquez M, Pascual-Montano A, Sorzano CO.
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W363-7. doi: 10.1093/nar/gkt385.

Scipion 1.0.0 – An Image Processing Framework for 3D Electron Microscopy

Scipion 1.0.0

:: DESCRIPTION

Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy (3DEM). It integrates several software packages and presents an unified interface for both biologists and developers.

::DEVELOPER

Biocomputing Unit – CNB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Xmipp

:: DOWNLOAD

  Scipion

:: MORE INFORMATION

Citation:

Scipion: a software framework toward integration, reproducibility and validation in 3D Electron Microscopy.
de la Rosa-Trevín JM, Quintana A, Del Cano L, Zaldívar A, Foche I, Gutiérrez J, Gómez-Blanco J, Burguet-Castell J, Cuenca-Alba J, Abrishami V, Vargas J, Otón J, Sharov G, Vilas JL, Navas J, Conesa P, Kazemi M, Marabini R, Sorzano CO, Carazo JM.
J Struct Biol. 2016 Apr 20. pii: S1047-8477(16)30079-X. doi: 10.1016/j.jsb.2016.04.010

A statistical approach to the initial volume problem in Single Particle Analysis by Electron Microscopy.
Sorzano CO, Vargas J, de la Rosa-Trevín JM, Otón J, álvarez-Cabrera AL, Abrishami V, Sesmero E, Marabini R, Carazo JM.
J Struct Biol. 2015 Mar;189(3):213-9. doi: 10.1016/j.jsb.2015.01.009.