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AGENDA
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
November 17-19, 2020
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
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