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Low budget 3D microscopy: how to create fascinating 3D transformations of a z-stack image series in microscopy and macroscopy

How can I visualise surface features such as wear and tear or surface roughness? How can I capture an image of an object under the microscope that makes it look as if it’s popping out from the screen?

In microscopy and macroscopy, focus stacking and the corresponding software tools are increasingly employed to extend the apparent depth of field of a photograph. Especially at higher magnifications of 30x, where, due to physical limits, the depth of field is very low, photographers often use focus stacking to improve depth of field. Over 100 separate photos are taken by gradually incrementing the focusing distance across the subject (this is the “z-stack”). With a specialised software, a composite image is then created, based on the sharpest regions from each of these separate photos.

We used a simple coin cell battery, available everywhere batteries are sold, for this process.

Helicon Focus 3D microfotography Box

These z-stacks can also be created by using a motorised focus rail (StackShot) and the Helicon Remote software. The finished z-stack, which contains more than 100 separate images, is then merged into one frame using the Helicon Fokus software. Because the image collection process is automated, all the images in the z-stack are captured with the same step size. It takes just a few mouse clicks and minutes of your time to create the finished image, which translates into significant improvements in workflow efficiency.

With our LM macroscopes and photomicroscopes, which are equipped with objective lenses that are optimised for this technique, it is possible to achieve the best possible image quality for each individual image. Achieving maximum resolution is a key aspect in the design of our devices.

LM makcroscope 24x with Stackshot Slider

The image above shows an LM macroscope with Cognisys StackShot system.

The LM macroscope has a central optical path and is thus considerably more powerful than comparable systems with a dual optical path or conventional stereomicroscopes. Thanks to its modular construction, it is extremely flexible and enables a multitude of magnification combinations (3x -> 18x), depending on which configuration of tube elements is used. The objective lenses are also available without a tripod.

Once the z-stack has been created, the rendering process can be started.

Helicon Focus 6.8. Rendering , 3d image

The data in the image file are then exported to create a 3D model with just one click.

Helicon Focus 3D rendering

The video above shows how a 3D model is created

Helicon’s “3D viewer” utility, which is included into the Helicon Focus installation, is designed to visualise 3D models. The object is displayed in a box, where it can be rotated and observed from any angle.

Helicon 3D data rotating

The 3D viewer supports almost all microscopic observation methods – bright field, dark field, incident light, fluorescence – at nearly any magnification.

Because DSLRs and system cameras have highly sophisticated camera sensors with up to 40 MP resolution and a huge dynamic range, it is possible to produce a highly accurate 3D dataset. We have compiled a set of camera recommendations to help you choose the DSLR that is best suited for your needs.


New LM Digital Adapter for: Sony Alpha 9 / Canon EOS R with Canon Adapter EF-EOS R / Sony Alpha 7R IV / Canon EOS RP with Canon Adapter EF-EOS R / Sony Alpha 7S II / Sony Alpha 7R III / Nikon Z6 with F-Mount Adapter FTZ / Sony Alpha 7R II / Nikon Z7 with F-Mount Adapter FTZ / Sony Alpha 7S / Nikon D850 / Canon EOS 1D X Mark II / Sony Alpha 7III / Nikon D5 / Sony Alpha 6400 / Canon EOS 1D X / Nikon D4s / Canon EOS 90D / Canon EOS 5D Mark IV / Nikon D4 / Nikon D750 / Canon EOS 6D Mark II / Sony Alpha 6300 / Sony Alpha 6500 / Nikon D500 / Nikon D810 / Nikon D800 / Nikon D800E / Nikon Df / Panasonic Lumix DC-G9 / Nikon D610 / Nikon D600 / Canon EOS 250D / Canon EOS M50 / Canon EOS 6D / Sony Alpha 99 II (SLT-A99 II) / Canon EOS 5DS R ( without low-pass filter) / Olympus OM-D E-M1 Mark II / Canon EOS 80D / Canon EOS 5DS / Sony Alpha 77 II / Canon EOS 70D / Nikon D7200 / Pentax K-1 Mark II / Canon EOS 200D / Canon EOS 800D / Rebel T7i / Canon EOS 77D / Canon EOS 5D Mark III / Canon EOS 60D / Sony Alpha 7R / Sony Alpha 7 /