<h1> Basic Processes in FIJI (Introduction to FIJI)</h1> <h2>Background</h2> This workshop provides a basic foundation to the open source image analysis program, [FIJJ][2] (FIJI Is Just ImageJ). It is intended for people who have never used the program before, or require a re-fresher on how to open images, merge channels, perform projections etc. <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. ---------- <h2>Topics Covered</h2> The intention of this workshop is to introduce new users to the program and covers the basic concepts around opening, saving and ethical manipulations to images. <br><br> - Opening/Saving/Closing Images (.tifs and Bio-Formats compatible files) - Merging channels, and dealing with multiple channel images - Adjusting Brightness & Contrast and using histograms - Adjusting bit-depth - Adding scale to images & adding scale bars - Image Stacks (Montages, Projections, Re-Slicing, Orthogonal Views) - Basic Measurements (Area, Intensity, Shape descriptors, Line Scans) - Creating Selections (Manual, ROI Manager) - Overlays ---------- <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: Open, Save & Close an Image <br> *Involves Opening a Bio-Formats image file and importing an Image Sequence series of files* - Exercise 2: Merging RGB Composite Images <br> *Involves taking 3 individual channel files (.tif) and combining them into a single multi-channel image.* - Exercise 3: Adjusting display bightness <br> *Involves correctly adjusting the display settings for the example image from Exercise 2.* - Exercise 4: Adding a scale bar <br> *Involves adding a scale bar to an image without a known scale (first adding scale to an image) and adding a scale bar to an image with a known scale.* - Exercise 5: Projecting 3D datasets <br> *Invovles reducing the dimensionality of 3D Z-stacks down to 2D MIPs.* - Exercise 6: Creating 3D Projections <br> *Involves making short animations to rotate a 3D dataset around the X, Y or Z axis.* - Exercise 7: Measuring Values from Images <br> *Involves measuring area and diameters of structures across different magnifications.* - Exercise 8: Performing a Line scan measurement <br> *Involves using the Plot profile tool to measure the FWHM of actin fibres in a STED and confocal image.* <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/31269/BasicProcessesFiji.png [2]: http://fiji.sc [3]: http://imb.uq.edu.au/microscopy