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Image analysis 1

Image analysis 1#

General information#

Main objective#

In this lesson you will learn about the foundation of image analysis. You will learn (i) basic concepts of image analysis such as image matrix, bit-depth, lookup table, histogram and threshold (ii) how to apply these concepts using ImageJ to proceed with image analysis.

Learning objectives#

Learning objective 1 - You can explain the following concepts

  • ImageJ & Fiji

  • image matrix

  • simplified image formation for fluorescent images

  • lookup table

  • image histogram

  • image normalization

  • conversions: 8- and 16-bit pseudo color images and 32-bit floating point images

  • threshold

Learning objective 2 - You can perform these operations using ImageJ

  • installing Fiji, updating it and adding plugins

  • peeking into image matrix using pixel inspection tool

  • changing lookup tables

  • displaying image histogram

  • changing the look of the image by using Image / Adjust / Brightness and Contrast tool

  • converting the image to 8/16/32-bits

  • applying Threshold

  • using Analyze Particles tool to count objects

Resources#

Completing of the image analysis part of the course requires accomplishing some exercises. All required images for these exercises should be downloaded from Github-ScopeM-teaching

Introduction to Bioimage Analysis#

The content presented here is adapted from the book Introduction to Bioimage Analysis by Pete Bankhead, which can be accessed in its entirety here. We have shared this material in compliance with the Creative Commons license CC BY 4.0, the details of which can be found here. While we have only made modifications to the formatting of the excerpts, we highly recommend reading the complete book for a deeper understanding of bioimage analysis.

Contents