How to Use Z-Stacking Microscopy SoftwareMicroscopy z-stacking software (also known as Extended Depth of Focus or EDF software) allows images to be captured under the microscope while focusing on different parts of the image, and then stacking them together into one clearly focused image. The Jenoptik microscopy cameras include z-stacking software. Below are instructions on how to capture a z-stack microscopy image.

Step 1: Capture Images

In order to create a z-stack, you must capture several images under the microscope at different focal depths. In order to do this place the sample beneath the microscope and capture image #1, slightly adjust the focal distance and capture image #2. Repeat as many times as you would like. The more images captured, the more detail your final z-stack image will reveal.

Image #1 shown below is a match head that was captured using the Zeiss Axio Scope.A1 microscope and a Jenoptik Subra microscope camera.

Jenoptik Subra microscopy image of Match Head


Image #2 below is the same match head captured with a different part of the match in focus.

Match head under a Zeiss microscope


Step 2: Perform Z-Stack in Software:

By using the software for z-stack (also referred to as extended depth of focus), you will simply let the software know which images you would like to use and it will then compile them into a final z-stack image.

This image is the z-stack of our captured match head images combined into one clearly focused image.

Z-Stack Microscopy Image of Match Head using Jenoptik Subra Camera

A few interesting facts about the head of a match!

The match was accidentally invented by an English chemist John Walker in 1826, when he was using a wooden stick to stir a mixture of starch, potassium chlorate, antimony sulfide and other ingredients. The match head is composed of sulfur (this is what you can smell) mixed with oxidizing agents like potassium chlorate, starch, powdered glass, dyes, fillers and binders. The glass creates friction with the glass in the safety paper, which ignites the head and then burns the wood.

If you have any questions extended depth of focus and Z-stacking microscopy software, contact Microscope World and we will be happy to help.