Module 1
Introduction to Digital Images
Basic concepts of digital images, file format, color scheme
Fundamentals of Image Processing
Histograms, displays, pixel adjustment, filters, kernels 
Fourier Transformation
Image processing in Fourier space
Module 2
Object-based Colocalization Analysis
​Quantifying overlapping objects
Pixel-based Colocalization and intensity Analysis
Colocalization coefficients, ratiometric imaging 
Analysis to track changes and movement
Fluorescence recovery rate, particle tracking, motion analysis
Object Segmentation
Turning pixel map into discrete objects
Module 3
Introduction to Fiji Macros
Basic programming concepts: variables, boolean logic, and user dialogs 
Intermediate Fiji Macros
Automating with loops, code reuse using functions, and summarizing data
Introduction to Machine Learning
ML for image processing
Object Segmentation with Machine Learning
Trainable Weka Segmentation in 2D and 3D
Image Restoration with Machine Learning
Introduction to CNNs and CARE

Advanced Imaging Center, HHMI Janelia Research Campus

FIJI Image Processing and Analysis Workshop

October 20-21, 2021

From HHMI Janelia Research Campus

Online Lectures
Download Links
FIJI Program
Click here to download for Mac
Click here to download for Windows
Click here to download for Linux
You should use this version even if you already have FIJI installed on your laptop. Do not update FIJI after installation.
Reading List
For additional reading, click here.
Macro Examples
Save this folder onto your desktop.
Sample Images
Save this folder onto your desktop