IMOD 4.9.12 – Tomographic 3D Reconstruction & Modeling

IMOD 4.9.12

:: DESCRIPTION

IMOD is a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3-D data from any orientation, and modeling and display of the image files.

::DEVELOPER

The Boulder Lab for 3D Electron Microscopy

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

IMOD ; source code

:: MORE INFORMATION

The citation is: Kremer J.R., D.N. Mastronarde and J.R. McIntosh (1996) Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 116:71-76. For tomographic reconstruction, see also: Mastronarde, D. N. (1997) Dual-axis tomography: an approach with alignment methods that preserve resolution. J. Struct. Biol. 120:343-352.

SerialEM 3.7.11 – Electron Tomography Data & Image Acquisition

SerialEM 3.7.11

:: DESCRIPTION

SerialEM is a program to acquire tilt series for electron tomography on Tecnai and JEOL microscopes. It uses an approach based on prediction of specimen position during the tilt series from the position at previous tilts. It does not count on the microscope or the specimen being particularly well-behaved, so unless a prediction appears reliable, it falls back to measuring and adjusting defocus and/or specimen position when necessary. With this method, it achieves both the robustness of the older approach to tilt series acquisition (track and focus at every tilt) and the speed of the newer precalibration approach. A 2Kx2K, 1 degree tilt series can be acquired in about 45 minutes with a single-port readout camera or 20-25 minutes with a four-port readout camera.

::DEVELOPER

The Boulder Lab for 3D Electron Microscopy

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

SerialEM

:: MORE INFORMATION

Citation:

Mastronarde, D.N. 2005.
Automated electron microscope tomography using robust prediction of specimen movements.
J. Struct. Biol.152:36-51.

GoIFISH 1.2 – Semi-automated Analysis of IFISH Images

GoIFISH 1.2

:: DESCRIPTION

GoIFISH has been developed for the analysis of IFISH (Immunofluorescence + Fluorescence in situ Hybridisation) images, performing nuclear, membrane and spot detection in order to quantify heterogeneity at the single cell level.

::DEVELOPER

the Markowetz lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • MatLab

:: DOWNLOAD

 GoIFISH

:: MORE INFORMATION

Citation

Genome Biol. 2014 Aug 26;15(8):442. doi: 10.1186/s13059-014-0442-y.
GoIFISH: a system for the quantification of single cell heterogeneity from IFISH images.
Trinh A, Rye IH, Almendro V, Helland A, Russnes HG, Markowetz F.

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)

Scipion 2.0 – An Image Processing Framework for 3D Electron Microscopy

Scipion 2.0

:: 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.

Giotto v0.1.4 – Single-cell Spatial Analysis pipeline

Giotto v0.1.4

:: DESCRIPTION

Giotto is a comprehensive pipeline for spatial transcriptomic data analysis and visualization.

::DEVELOPER

Guo-CHeng Yuan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • R
  • ImageJ library (JAR file)

:: DOWNLOAD

Giotto

:: MORE INFORMATION

Citation

Giotto, a pipeline for integrative analysis and visualization of single-cell spatial transcriptomic data
Ruben Dries, Qian Zhu, Chee-Huat Linus Eng, Arpan Sarkar, Feng Bao, Rani E George, Nico Pierson, Long Cai, Guo-Cheng Yuan
doi: https://doi.org/10.1101/701680

EM-SURFER – Navigating 3D Electron Microscopy Maps

EM-SURFER

:: DESCRIPTION

EM-SURFER is a web platform for real-time electron microscopy database search. It compares isosurface shape of a query EM map against maps in the latest EMDB.

::DEVELOPER

Kihara Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Navigating 3D electron microscopy maps with EM-SURFER.
Esquivel-Rodríguez J, Xiong Y, Han X, Guang S, Christoffer C, Kihara D.
BMC Bioinformatics. 2015 May 30;16:181. doi: 10.1186/s12859-015-0580-6.

pyHIVE 1.0.8 – Health-related image visualization and engineering system using Python

pyHIVE 1.0.8

:: DESCRIPTION

pyHIVE was implemented as an image processing system, providing five widely used image feature engineering algorithms.

::DEVELOPER

Health Informatics Lab (HILab)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • Python

:: DOWNLOAD

pyHIVE

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2018 Nov 26;19(1):452. doi: 10.1186/s12859-018-2477-7.
pyHIVE, a health-related image visualization and engineering system using Python.
Zhang R, Zhao R, Zhao X, Wu D, Zheng W, Feng X, Zhou F.

GroupTracker 1.0.1 – Video Tracking system for multiple Animals under Severe Occlusion

GroupTracker 1.0.1

:: DESCRIPTION

GroupTracker (GROUP: Gaussian Reinterpretation of OcclUsion Problem) is a multiple animal tracking system that tracks individuals under severe occlusion.

::DEVELOPER

Tsukasa Fukunaga

::REQUIREMENTS

  • Linux
  • UMATracker

:: DOWNLOAD

GroupTracker

:: MORE INFORMATION

Citation

Comput Biol Chem. 2015 Aug;57:39-45. doi: 10.1016/j.compbiolchem.2015.02.006.
GroupTracker: Video tracking system for multiple animals under severe occlusion.
Fukunaga T, Kubota S, Oda S, Iwasaki W.

Dapple 0.88pre4 – DNA Microarrays Image Analysis

Dapple 0.88pre4

:: DESCRIPTION

Dapple is a program for quantitating spots on a two-color DNA microarray image. Given a pair of images from a comparative hybridization, Dapple finds the individual spots on the image, evaluates their qualities, and quantifies their total fluorescent intensities.

Dapple is designed to work with microarrays on glass. The spot-finding techniques used are robust to uneven spot sizes and positional deviations caused by “wobbling” of the arraying robot, as well as image noise and artifacts. As long as your spots are consistently circular, Dapple has a good chance of finding them accurately.

::DEVELOPER

Jeremy Buhler

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

Dapple

:: MORE INFORMATION

Citation:

J. Buhler, T. Ideker, D. Haynor, “Dapple: Improved Techniques for Finding Spots on DNA Microarrays”, University of Washington Department of Computer Science & Engineering Technical Report UW-CSE-2000-08-05, (2000)  Supplement.