Imagej (19)#
A Fiji Scripting Tutorial#
Albert Cardona
Licensed CC0-1.0
Tags: Imagej, Bioimage Analysis
Content type: Notebook
A study on long-term reproducibility of image analysis results on ImageJ and Fiji#
Robert Haase, Deborah Schmidt, Wayne Rasband, Curtis Rueden, Florian Jug, Pavel Tomancak, Eugene W. Myers
Tags: Imagej
Content type: Publication, Poster
https://figshare.com/articles/poster/I2K_Poster_Haase_V6_ImageJ_repro_pdf/7409525
CLIJ: GPU-accelerated image processing for everyone#
Robert Haase, Loic Royer, et al.
Published 2020
Licensed ALL RIGHTS RESERVED
CLIJ is a collection of image processing functions that use graphics processing units for accelerated processing.
Tags: Imagej, Bioimage Analysis
Content type: Publication
Fiji#
Licensed BSD-2-CLAUSE
Fiji is a popular free open-source image processing package based on ImageJ.
Tags: Imagej, OMERO
Content type: Online Tutorial
https://omero-guides.readthedocs.io/en/latest/fiji/docs/index.html
ImageJ2 API-beating#
Robert Haase
Licensed BSD-3-CLAUSE
Tags: Neubias, Imagej, Bioimage Analysis
Content type: Slide
Introduction to Bioimage Analysis#
Pete Bankhead
Licensed CC-BY-4.0
Tags: Python, Imagej, Bioimage Analysis
Content type: Book, Notebook
Introduction to Image Analysis with Fiji#
Robert Haase, Benoit Lombardot
Licensed CC-BY-NC-4.0
Tags: Imagej, Fiji, Bioimage Analysis
Introduction to ImageJ macro programming, Scientific Computing Facility, MPI CBG Dresden#
Robert Haase, Benoit Lombardot
Licensed UNKNOWN
Tags: Imagej, Bioimage Analysis
Content type: Slide
JIPipe: visual batch processing for ImageJ#
Ruman Gerst, Zoltán Cseresnyés, Marc Thilo Figge
JIPipe is an open-source visual programming language for easy-access pipeline development
Tags: Workflow Engine, Imagej
Content type: Publication, Documentation
KNIME Image Processing#
None
Licensed GPLV3
The KNIME Image Processing Extension allows you to read in more than 140 different kinds of images and to apply well known methods on images, like preprocessing. segmentation, feature extraction, tracking and classification in KNIME.
Tags: Imagej, OMERO, Bioimage Data, Workflow
Content type: Tutorial, Online Tutorial, Documentation
Lecture Applied Bioimage Analysis 2020#
Robert Haase
Slides, scripts, data and other exercise materials of the BioImage Analysis lecture at CMCB TU Dresden 2020
Tags: Imagej, Bioimage Analysis
Content type: Slide
https://git.mpi-cbg.de/rhaase/lecture_applied_bioimage_analysis
MiToBo - A Toolbox for Image Processing and Analysis#
Birgit Möller, Markus Glaß, Danny Misiak, Stefan Posch
The Microscope Image Analysis Toolbox is a toolbox with a collection of algorithms for processing and analyzing digital images.
Tags: Workflow Engine, Imagej
Content type: Publication, Documentation
https://openresearchsoftware.metajnl.com/articles/10.5334/jors.103
ModularImageAnalysis (MIA): Assembly of modularisedimage and object analysis workflows in ImageJ#
Stephen J. Cross, Jordan D. J. R. Fisher, Mark A. Jepson
ModularImageAnalysis is a Fiji plugin providing a modular framework for assembling image and object analysis workflows
Tags: Workflow Engine, Imagej
Content type: Publication, Documentation
Multi-view fusion#
Robert Haase
Licensed BSD-3-CLAUSE
Lecture slides of a session on Multiview Fusion in Fiji
Tags: Neubias, Imagej, Bioimage Analysis
Content type: Slide
https://git.mpi-cbg.de/rhaase/lecture_multiview_registration
Plugin “omero-batch-plugin”#
Licensed GPL-2.0
An ImageJ plugin to run a script or macro on a batch of images from/to OMERO.
Tags: OMERO, Imagej, Imagej Macro, Github
Content type: Github Repository
The Fiji Updater#
Robert Haase
Licensed ALL RIGHTS RESERVED
Article about the Fiji Updater explaining how it works in the background.
Tags: Imagej
Content type: Publication
https://analyticalscience.wiley.com/do/10.1002/was.0004000112/
Tracking Theory, TrackMate, and Mastodon#
Robert Haase
Licensed BSD-3-CLAUSE
Lecture slides of a session on Cell Tracking in Fiji
Tags: Neubias, Imagej, Bioimage Analysis
Content type: Slide
Working with objects in 2D and 3D#
Robert Haase
Licensed BSD-3-CLAUSE
Tags: Neubias, Imagej, Bioimage Analysis
Content type: Slide
https://git.mpi-cbg.de/rhaase/lecture_working_with_objects_in_2d_and_3d
Working with pixels#
Robert Haase
Licensed BSD-3-CLAUSE
Tags: Neubias, Imagej, Bioimage Analysis
Content type: Slide
https://git.mpi-cbg.de/rhaase/lecture_working_with_pixels