# Imagej (20) ## A Fiji Scripting Tutorial Albert Cardona Licensed CC0-1.0 Tags: Imagej, Bioimage Analysis, Include In Dalia Content type: Notebook [https://syn.mrc-lmb.cam.ac.uk/acardona/fiji-tutorial/](https://syn.mrc-lmb.cam.ac.uk/acardona/fiji-tutorial/) --- ## 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, Exclude From Dalia Content type: Publication, Poster [https://figshare.com/articles/poster/I2K_Poster_Haase_V6_ImageJ_repro_pdf/7409525](https://figshare.com/articles/poster/I2K_Poster_Haase_V6_ImageJ_repro_pdf/7409525) --- ## ABIC - Intermediate Fiji Image Analysis Course 2024 Rensu Petrus Theart Licensed CC-BY-4.0 A structured beginner to intermediate-level course in image analysis using Fiji, developed for ABIC 2024. It includes a video lecture playlist, course documentation, and participant image files. Tags: Bioimage Analysis, Image Processing, Teaching Resource, Imagej, Exclude From Dalia Content type: Workshop, Video, Document [https://www.youtube.com/playlist?list=PL0RrV4sTNwh2S9Lb7d1TzJWPGgdw_YVnb](https://www.youtube.com/playlist?list=PL0RrV4sTNwh2S9Lb7d1TzJWPGgdw_YVnb) [https://docs.google.com/document/d/1h-3oJDR7gd_y3tfgN3clPwt2O4g34QRPp_FJ4v2Q7kA/edit?usp=sharing](https://docs.google.com/document/d/1h-3oJDR7gd_y3tfgN3clPwt2O4g34QRPp_FJ4v2Q7kA/edit?usp=sharing) [https://www.dropbox.com/scl/fi/7njq2wp680vubt6rwhn5f/ParticipantImages.zip?rlkey=pk3kttbsclk69ixxp1yv9j8p3&dl=0](https://www.dropbox.com/scl/fi/7njq2wp680vubt6rwhn5f/ParticipantImages.zip?rlkey=pk3kttbsclk69ixxp1yv9j8p3&dl=0) --- ## 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, Exclude From Dalia Content type: Publication [https://doi.org/10.1038/s41592-019-0650-1](https://doi.org/10.1038/s41592-019-0650-1) --- ## Fiji Licensed BSD-2-CLAUSE Fiji is a popular free open-source image processing package based on ImageJ. Tags: Imagej, OMERO, Exclude From Dalia Content type: Online Tutorial [https://omero-guides.readthedocs.io/en/latest/fiji/docs/index.html](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, Include In Dalia Content type: Slides [https://git.mpi-cbg.de/rhaase/lecture_imagej2_dev](https://git.mpi-cbg.de/rhaase/lecture_imagej2_dev) --- ## Introduction to Bioimage Analysis Pete Bankhead Licensed CC-BY-4.0 Tags: Python, Imagej, Bioimage Analysis, Include In Dalia Content type: Book, Notebook [https://bioimagebook.github.io/index.html](https://bioimagebook.github.io/index.html) --- ## Introduction to Image Analysis with Fiji Robert Haase, Benoit Lombardot Licensed CC-BY-NC-4.0 Tags: Imagej, Fiji, Bioimage Analysis, Include In Dalia [https://github.com/mpicbg-scicomp/CourseIntroToIA](https://github.com/mpicbg-scicomp/CourseIntroToIA) --- ## Introduction to ImageJ macro programming, Scientific Computing Facility, MPI CBG Dresden Robert Haase, Benoit Lombardot Licensed UNKNOWN Tags: Imagej, Bioimage Analysis, Include In Dalia Content type: Slides [https://git.mpi-cbg.de/scicomp/bioimage_team/coursematerialimageanalysis/tree/master/ImageJMacro_24h_2017-01](https://git.mpi-cbg.de/scicomp/bioimage_team/coursematerialimageanalysis/tree/master/ImageJMacro_24h_2017-01) --- ## 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, Exclude From Dalia Content type: Publication, Documentation [https://www.nature.com/articles/s41592-022-01744-4](https://www.nature.com/articles/s41592-022-01744-4) [https://jipipe.hki-jena.de/](https://jipipe.hki-jena.de/) --- ## KNIME Image Processing None Licensed GPL-3.0 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, Workflow, Exclude From Dalia Content type: Tutorial, Online Tutorial, Documentation [https://www.knime.com/community/image-processing](https://www.knime.com/community/image-processing) --- ## 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, Include In Dalia Content type: Slides [https://git.mpi-cbg.de/rhaase/lecture_applied_bioimage_analysis](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, Exclude From Dalia Content type: Publication, Documentation [https://openresearchsoftware.metajnl.com/articles/10.5334/jors.103](https://openresearchsoftware.metajnl.com/articles/10.5334/jors.103) [https://mitobo.informatik.uni-halle.de/](https://mitobo.informatik.uni-halle.de/) --- ## 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, Exclude From Dalia Content type: Publication, Documentation [https://doi.org/10.1111/jmi.13227](https://doi.org/10.1111/jmi.13227) [https://mianalysis.github.io/](https://mianalysis.github.io/) --- ## Multi-view fusion Robert Haase Licensed BSD-3-CLAUSE Lecture slides of a session on Multiview Fusion in Fiji Tags: Neubias, Imagej, Bioimage Analysis, Include In Dalia Content type: Slides [https://git.mpi-cbg.de/rhaase/lecture_multiview_registration](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, Exclude From Dalia Content type: Github Repository [https://github.com/GReD-Clermont/omero_batch-plugin](https://github.com/GReD-Clermont/omero_batch-plugin) --- ## The Fiji Updater Robert Haase Licensed ALL RIGHTS RESERVED Article about the Fiji Updater explaining how it works in the background. Tags: Imagej, Exclude From Dalia Content type: Publication [https://analyticalscience.wiley.com/do/10.1002/was.0004000112/](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, Include In Dalia Content type: Slides [https://git.mpi-cbg.de/rhaase/lecture_tracking_trackmate](https://git.mpi-cbg.de/rhaase/lecture_tracking_trackmate) --- ## Working with objects in 2D and 3D Robert Haase Licensed BSD-3-CLAUSE Tags: Neubias, Imagej, Bioimage Analysis, Include In Dalia Content type: Slides [https://git.mpi-cbg.de/rhaase/lecture_working_with_objects_in_2d_and_3d](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, Include In Dalia Content type: Slides [https://git.mpi-cbg.de/rhaase/lecture_working_with_pixels](https://git.mpi-cbg.de/rhaase/lecture_working_with_pixels) ---