Below are lecture recordings and sample files from the Microscopy Workshop this past summer.

Module 1: Introduction

Why should one learn automated image processing?
Case study on how automated image processing can save time & effort
Cautions with digital image processing

Please go here to view tips for imaging at optimal imaging settings.

Module 2: Removing background & noise, carrying out particle analysis

Module 3: Deconvolution, 3D visualization and colocalisation analysis

Module 4: Macro Programming

Useful Bits of Code

Select a particular image:


Select a particular slice in a stack:


Pause and wait:

waitForUser(“instructions here”); 

To close a window:

run("Close"); or close(); 

Get the name of an image:


To run a block of code on a number of stacks:

for (i=1; i<=nSlices; i++){ insert lines of code }

Please feel free to contact us if you have any questions, comments or suggestions.