What is Automated Microscopy?

As microscopy advances, it gains opportunities to introduce compelling technology from other sectors to improve workflows and data acquisition. The ability to automate aspects of microscopy offers several benefits to data acquisition, such as real-time evaluation and immediate archival. 

In addition, the automation of hardware preserves samples within sterile conditions for human life, such as extreme temperatures or imbalances in carbon dioxide. Because the microscope captures images of samples without the touch of a person, the hardware is left within those conditions while a researcher sits a safe distance and conducts data collection.

This article will discuss how microscope components are altered to support automation and what you should prepare in terms of computing power and software to help operate one of these devices. 

When Did Automated Microscopy Done First?

The automation of image analysis began in 1962 when Metals Research of Cambridge, England, developed a television-based analyzer of microscope images. 

According to Leica-Microsystems, this was called the QTM (Quantitative Television Microscope) and featured a fully analog setup with multiple television screens, and measurements manually read from a meter. While primitive compared to today’s standards, this led to the development of the QTM B, which commercially launched the next year and was financially successful.

Building off the QTM A and B, researchers continued developing computer and automated microscopy solutions, even if they worked at minimal resolution and had to develop early post-processing situations before photoshop’s introduction. 

In tandem, optical microscopy solutions continued evolving, as computing power did overall. But these optical microscopes were capable of producing results far better than digital implements at the time, despite using the same research-grade lens equipment

Many were waiting for the technology to advance and rival traditional microscopy, hoping to further research procedures and science as a whole. 

This advancement has occurred, and fully digital implements produce results greater than counterparts with more advanced components than those in traditional compound microscopes.

What Hardware is in an Automated Microscope?

While an automated microscope features the same key components as a standard digital microscope, these are tuned and changed to work with automation processes. 

This change means that individual parts of the microscope have their controls that must work in time with other device elements to all function properly. With some help from Bite-Size Bio, let’s go through some of these one at a time.


Multiple electromechanical shutters block differing light sources from illuminating the specimen. This is particularly important as a function when capturing images of live specimens, as these are sensitive to photobleaching and phototoxicity, and therefore should be exposed to very minimal lighting. 

These are controlled via a microprocessor and directly with a computer to work in tandem with other camera elements in an automation setting. These specifically are responsible for casting light down on the subject between camera exposures and will also decide which light source should be cast on the specimen. 

Wavelength Selection

Opposed to our shutters, which filter out certain light channels, our wavelength selection is often a moving mechanism introducing colored filters into our lights for use with multichannel and spectral imaging systems. 

This is a much faster solution than having a researcher manually switch these filters out; however, there are known drawbacks. Primarily these mechanisms are controlled by physical components that vibrate, which is disruptive to certain specimens and samples. 

Additionally, while their speed is high, it is finite, and so you must be aware of these limitations if you are looking for continuous image capture. 

Focus and Stage Control

These mechanical controls enable the stage’s moving in x, y, and z axes to properly position the specimen and the lenses meant to capture it. This is all controlled through our software solution, which ensures that the image will contain maximum clarity through autofocusing. 

These motorized techniques are currently used in advanced digital microscopes, so if you work with a computer-connected microscope before, you may be familiar with this technology and its interfaces. 

Light Sources

Automated microscopy solutions can employ multiple lighting solutions, sometimes even simultaneously. This includes halogen, laser, and arc gas light sources that all offer different wavelengths of light and varying brightness levels. 

Advanced software solutions can handle the transitions between light sources by choreographing them ahead of time, or researchers can manually adjust lights as needed.

Camera & Detection System

Software solutions manually operate the camera or detector used to capture images for use via software. This means that the software controller triggers the shutter automatically once the specimen is positioned correctly, without any manual input from a person. 

As with other processes, researchers can also operate these systems manually if they are working to demonstrate or seek specific results.  In either case, the camera shutter activates, allowing it to capture light through a research-grade objective lens and produce a high-quality digital image. 

Carbon Dioxide and Temperature Control

Automated microscopes can exist within a temperature and atmosphere-controlled environment where humans require the protective covering to survive. 

As such, these microscopes can monitor conditions and adjust as necessary while researchers survey them in a separate space. This enables the researchers to maintain safety while also keeping their samples within the conditions required to preserve them for imaging and documentation properly. 

What Computer Should I Use With My Automated Microscope?

Automated microscopy is a complicated process, and as such, it needs a computer that can process and store the data that it is generating. As MicroscopyU explains, a safe starting point for a computer for automated microscopy is one with a three gigahertz Central Processing Unit (CPU) and at least one gigabyte of Random Access Memory.


As storage space has become relatively affordable, it should be easy to acquire a storage drive with at least 250 gigabytes of storage, particularly in a solid-state or even NVMe format which has immensely high read and write speeds. If your application requires it, you can also consider installing an optical disk drive to write data onto CDs or DVDs; however, these mediums are only valuable for the physical storage of data and not for quick or frequent transferring.


When assembling or acquiring an automated microscope, it is important to know what type of connector it uses to attach itself to your computer. While some will use standard USBs, others might require FireWire, RS-422, or SCSI ports to connect. Not only that, but some manufactured solutions include proprietary ports and cables that only work with circuit boards sent from the manufacturer. 

In this case, you need to ensure that the computer components you’re acquiring are compatible with this specific motherboard; otherwise, there could be issues. Additionally, you should ensure that your graphics hardware can output to your monitor of choice, which should be in at least standard high definition. 

These connections are typically through HDMI or Displayport, so ensure that the ports on your computer and your display match.

Software & Apps

In terms of software or applications, most digital camera systems include these. They can perform simple tasks and adjust camera settings like exposure time, offset, and gain. The complexity and depth of these vary by manufacturer, so ensure that your provider can help supply some of the best software available. 

Ideally, your software solution can assist with post-processing for brightness and contrast or even offer assistance for post-acquisition analysis like acquiring complex measurements to drive optimal machine vision results. In the best-case scenarios, these can also include a software development kit to customize your tools if needed and extract the data you specifically need.  


Automated microscopes are complicated devices with several interacting components and software solutions to choreograph them for staging specimen photos in various lighting or magnification conditions. 

While this sounds daunting, it is the natural evolution of microscopy technology as scientific procedures continue to utilize digital platforms for greater value. This article provides you with a general overview of the hardware involved in microscopy automation and some of the other required preparations to adopt this innovative new method. 

As you search for solutions to meet your application, be sure to consider not just your selected components but their compatibility with one another to ensure minimal disruption to your processes.


Lecia-Microsystems - 50 Years of Image Analysis | Lecia-microsystems.com

Bite Size Bio - Automated Microscopy | Bitesizebio.com

MicroscopyU - The Automatic Microscope | Microscopyu.com

Association for Advancing Automation - What is Automated Microscopy and How Does it Work? | Automate.org

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