<h1> Advanced FIJI</h1> <h2>Background</h2> This workshop is designed for users who want to automatically process and quantify images using the open source image analysis program, [FIJJ][2] (FIJI Is Just ImageJ). It is intended for people who are familiar with the program. <br><br> FIJI is an open source image analysis program which builds upon ImageJ as it comes 'batteries included' meaning extra plugins and libraries are included by default for an easy installation. The software works on Windows, Mac & Linux and can be run headless on HPC. <br><br> This workshop is now available to view on [Youtube][3]. ---------- <h2>Topics Covered</h2> The intention of this workshop is to introduce users to the automation tools in FIJI including Plugins, Batch Processing and Scripting. <br><br> Using Other People's tools for automation<br> - Installing and Updating Plugins - Visualisation Plugins: [3D Viewer][4], [Big Data Viewer][5] & [Clear Volume][6] - Segmentation Plugin: [StarDist][7] - Tracking Plugin: [TrackMate][8]<br><br> Creating your own automation - Finding commands in FIJI - Batch Processing - Scripting ---------- <h3> Example exercises in this workshop </h3> In addition to slides and descriptive examples of key concepts the workshop includes worked examples for attendees to gain hands on experience with. This are listed below.<br><br> - Exercise 1: Installing Plugins <br> *Involves correctly finding and updating plugins relevant for the workshop.*<br><br> - Exercise 2: Trying 3D Volume Viewers <br> *Involves exploring using the three volume viewing plugins (3D_Viewer, Big Data Viewer & Clear Volume) with 3D example data-sets.*<br><br> - Exercise 3: Explore Deep Learning plugin StarDist <br> *Involves segmenting nuclei using deep learning algorithms via the StarDist plugin.*<br><br> - Exercise 4: Trackmate worked example <br> *Involves using the TrackMate plugin to segment and track swimming algae.*<br><br> - Exercise 5: Batch Processing <br> *Involves identifying commands and using the batch processing process to automate simple tasks.*<br><br> - Exercise 6: Running a script <br> *Involves installing and running a custom written script to process a folder of images automatically.*<br><br> <h2> Content Files included in this Project</h2> - PDF document of slides (1pp) - PDF document of slides-Handouts (3pp) - PPT file containing slides - Example exercise files (.zip) ---------- <h3> About the Author </h3> Dr Nicholas Condon is a Senior Microscopist and CZI Imaging Scientist at The University of Queensland's Institute for Molecular Bioscience working in the Microscopy Core Facility.<br> For more information visit: https://imb.uq.edu.au/microscopy [1]: https://imb.uq.edu.au/files/31254/AdvanceProcessesFiji.png [2]: http://fiji.sc [3]: https://youtu.be/s4sfWZRdSjs [4]: https://imagej.net/3D_Viewerji.png [5]: https://imagej.net/BigDataViewer [6]: https://imagej.net/ClearVolume [7]: https://imagej.net/StarDist [8]: https://imagej.net/TrackMate