<h1> Intermediate FIJI</h1> ![IntermediateBanner][1] <h2>Background</h2> This workshop is designed for users who want to 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. ---------- <h2>Topics Covered</h2> The intention of this workshop is to introduce users to the processes and tools available to filter, segment and measure image data. The workshop is broken into 3 subsections, Pre-Processing, Segmentation, Analysis <br><br> Pre-Processing image data<br> * Filtering (Mean, Median, etc) * Background Subtraction * Math Segmentation * Thresholding * Colour Thresholding * Watersheding * Generating ROIs (manually & automatically using Analyze Particles) * Finding Maxima * Image Calculations Analysis * Measurements in FIJI * Shape Descriptors * Plot Profiles (Line Scans) * LUTs ---------- <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: Performing Background Subtraction <br> *Involves coorectly measuring objects shortest width to implement a rolling ball background subtraction.*<br><br> - Exercise 2: Thresholding <br> *Involves exploring using the threshold tool on both a gradient image as well as segmenting DAPI stained nuclei using different auto thresholds.*<br><br> - Exercise 3: Colour Thresholding <br> *Involves segmenting regions of interest in colour histology images.*<br><br> - Exercise 4: Adding Nuclei to the ROI manager <br> *Involves filtering a nuclei image, performing a threshold and analysing particles to automatically add selections to the ROI manager.*<br><br> - Exercise 5: Finding Maxima <br> *Invovles creating segmentations based upon the Find Maxima tool.*<br><br> - Exercise 6: Making a mask of GFP expressing cells <br> *Involves creating a threshold of one channel and using it as a mask for another channel of the same image (eg. Masking for only GFP expressing cells).*<br><br> - Exercise 7: FRET Calculation <br> *Involves performing a FRET/Donor image calculation by splitting channels, creating a mask and performing an image calculation, followed by adjusting the LUT and performing a measurement.* <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/31260/IntermediateProcessesFiji.png [2]: http://fiji.sc