This module invites you to learn fundamentals of image analysis by viewing two videos delivered by Christian Tischer (EMBL, Heidelberg, Germany) and Nicholas Condon (Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia).
Presenter: Nicholas Condon, Institute for Molecular Bioscience, The University of Queensland, Australia
Presenter: Christian Tischer, EMBL, Germany
This free of charge course on edX platform covers basic image analysis for life scientists. This course will teach you necessary steps from image acquisition to image filtering and segmentation. In addition, open source software solutions will be demonstrated as part of this course. For a detailed overview of the course and the learning objectives, head out to edX platform where this course is delivered.
This module invites you to learn about image analysis software ImageJ and its more powerful version, Fiji, that features plugins that aid in image processing and analysis.
ImageJ is an open source image processing and analysis software that is specifically designed for processing and analysis of scientific multidimensional (2D-4D) images. ImageJ, in addition to its baseline functionality, can be customized with thousands of plugins and scripts allowing it to perform a wide variety of processing and analysis tasks within many scientific communities.
Fiji is a distribution of ImageJ that contains large number of up-to-date curated plugins that greatly facilitate image analysis. In addition to being useful to users, Fiji can also be used by developers since Fiji is an open source project hosted in a Git version control repository, with access to the source code of all internals, libraries and plugins, and eases the development and scripting of plugins.
Presenter: Kevin Eliceiri, University of Wisconsin–Madison, Madison, United States
Presenter: Nicholas Condon, Institute for Molecular Bioscience, The University of Queensland, Australia
Presenter: Nicholas Condon, Institute for Molecular Bioscience, The University of Queensland, Australia
The ImageJ User Guide guide provides a detailed overview of ImageJ and Fiji. The user guide is available as HTML version and as a PDF document.
The ImageJ User Guide guide provides a detailed overview of ImageJ and Fiji. The user guide is available as HTML version and as a PDF document.
Image.sc forum is a message board intended to help those with image processing and analysis-related questions to find a workable solution.
This module invites you to learn about image analysis software CellProfler.
CellProfiler is a free, open-source software that allows to produce quantitative measurements of phenotypes from thousands of images automatically.
Presenter: Anne Carpenter, Broad Institute of MIT and Harvard, USA
Presenter: Beth Cimini, Broad Institute of MIT and Harvard, USA
Presenter: David Stirling, Glencoe Software
This workshop covers integration of CellProfiler with other open source tools such as CellProfiler Analyst, Ilastik, ImageJ, and Cellpose.
Download and learn more about CellProfiler at the link above.
Extensive list of CellProfile tutorials in video and PDF format.
Introduction to CellProfiler: iBiology Techniques YouTube channel
Introduction to CellProfiler Workshop, Advanced CellProfiler Workshop: Center for Open Bioimage Analysis YouTube channel
This module invites you to learn about image analysis software CellProfler Analyst, a free image analysis software for high-throughput imaging.
CellProfiler Analyst allows interactive exploration and analysis of multidimensional data from high-throughput, image-based experiments. Its most popular feature is a supervised machine learning system called Classifier that can be trained to recognize complicated and subtle phenotypes, for automatic scoring of millions of cells.
Presenter: Rebecca Senft, Broad Institute of MIT and Harvard, USA
Tutorials focused on CellProfiler and CellProfiler Analyst, developed by the Center for Open Bioimage Analysis.
Download and learn more about CellProfiler Analyst at the link above.
This module invites you to explore Microscopy Image Browser (MIB), a free to use image analysis software for electron microscopy data.
Microscopy Image Browser (MIB) is an image analysis MATLAB-based software ideally suited for segmentation and visualization of multi-dimensional (2D-4D) light and electron microscopy data. It is available for free.
Presenter: Ross Laws, Newcastle University, Newcastle upon Tyne, United Kingdom
Presenter: Ross Laws, Newcastle University, Newcastle upon Tyne, United Kingdom
Presenter: Ilya Belevich, University of Helsinki, Helsinki, Finland
Tutorials focused on Microscopy Image Browser, covering a wide range of topics including introduction, image segmentation, visualization, tools, and programming.
Download and learn more about Microscopy Image Browser at the link above.
This modules provides an in-depth instructions at how to use IMARIS for image analysis and visualization.
Imaris is an image analysis and visualization software that can be used for visualization, analysis and interpretation of 2D, 3D, and 4D microscope images. Imaris is able to detect and model biologically relevant structures using step-by-step wizards with a preview of the results at each point of the workflow.
Imaris learning resource is a public resource that contains videos and PDF documents that describe operation of Imaris and applications of Imaris in analyzing image data obtained from various cell lines and model organisms. Videos and PDF documents can be sorted by applications, content type, product families, and products.
This project has been made possible in part by a grant from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation.
