Important Terms for In Situ Microscopy

In situ microscopy is an investigatory method which permits researchers to see how a sample reacts to stimuli under an electron microscope. Researchers were not able to witness real-time effects before in situ microscopy which meant they were blind to processes and reactions whilst they happened and could only observe end results.

In situ microscopy can be utilized to observe reactions in a number of research areas including:

  • Materials characterization
  • Catalysis
  • Batteries
  • Life sciences and many others

In situ microscopy is a complicated technique that involves numerous tools and processes, plus training for microscope operations and advanced scientific study. The real-time observational potential of in situ microscopy has assisted revolutionary discoveries in various areas of study. This glossary can clarify in situ microscopy terms for those who are new to the research method.


A vacuum means the absence of matter within an enclosed volume. The strength of the vacuum relates to the number of particles remaining in the volume. High to ultra-high vacuum conditions are needed for electron microscopy.


Materials that measure between 1 and 100 nanometers (nm) in size are defined as nanoparticles.

Transmission Electron Microscope (TEM)

This is a type of electron microscope that utilizes a high voltage electron beam, emitted by a cathode and created by using magnetic lenses. The electron beam is transferred through the specimen at the same time, which creates an image that can illuminate the size and structure of the sample. Afterward magnetic lenses enlarge the image and capture a two-dimensional, black and white digital image which can be displayed in real-time on a computer monitor.

Electron Microscope (EM)

By imaging samples with a beam of electrons, an electron microscope can allow magnifications hundreds to thousands of times bigger than light microscopes. They are widely utilized by researchers to examine fine detail in a variety of samples and Ems typically need trained personnel to operate them.

Environmental TEM (ETEM)

The products and practices employed to introduce a gaseous environment into a TEM are described as ETEM. First introduced as a microscope equipped with gas nozzles that would permit researchers to pump gas into the sample, now ETEM is mostly utilized as specialized in situ microscopy holders that allow for the study of native gas environments.

TEM Holder

TEM holders are instruments employed inside an electron microscope to house and support a sample. In situ TEM holders can change the sample’s environment (by gas, liquid, or heat) to enable native sample study.

Liquid Cell

A liquid cell is a tool that keeps samples encased inside a liquid environment within an electron microscope. A liquid cell in situ TEM holder must be used by researchers to study native liquid cells under electron microscopes.

Gas Cell

A gas cell is a device that encases samples within a gaseous environment within an electron microscope. Traditionally, electron microscopes have required vacuum conditions, so researchers must use specialized gas cell in situ TEM holders to examine gas cells under electron microscopes.

Scanning Electron Microscope (SEM)

A scanning electron microscope (SEM) directs an electron beam at a sample and captures an image based on elastically or inelastically scattered electrons emitted via excitation from the surface of the sample. In this type of microscope, the electron beam scans across the sample in a raster pattern, and an image is created from the signals detected during the scanning process.

Scanning Transmission Electron Microscope (STEM)

A scanning transmission electron microscope (STEM) is a combination of TEM and SEM methods; an electron beam is projected through a sample like a TEM. But, like an SEM, the electron beam travels through incremental areas, an image is generated by combining data from these small sections which is then compiled and displayed in real-time on a monitor.


Another term for “in situ” is operando. Although, in situ refers to changing the sample environment, while operando is specifically imitating the environment of a real application.

Microelectromechanical Systems (MEMS)

MEMS incorporate microsensors and microactuators, which are transducers that convert energy from one form into another. Normally, this involves converting a mechanical signal into an electrical signal.

MEMS are employed in electron microscopes to alter the sample environment of experiments. MEMS are a technology defined as miniaturized electro-mechanical and mechanical parts made with microfabrication.

Energy-Dispersive X-Ray Spectroscopy (EDS)

A technique which is used for chemical characterization of a sample is EDS. Each element emits characteristic x-rays when exposed to a high energy electron beam, so this method can establish the composition of samples. EDS can be employed in SEM, STEM, and electron microscopes.

  • EDS Detector
    This device is employed for EDS chemical characterization. x-ray energy is converted into voltage signals, which are then conveyed to a pulse processor. The pulse processor calculates the signals and passes them on for analysis and data display.

Sample Support

Sample supports come in a large selection of shapes and sizes, and use many different materials as the support structure. Traditionally, the minuscule sample size needed for TEM analysis requires samples to be supported by some structure so that they do not fall into the vacuum of the TEM.

  • E-chips
    E-chips are the proprietary name for Protochips MEMS-based sample supports. They are employed to support and confine in situ samples. E-chips are used for in situ TEM holders, including Protochips’ Fusion, Atmosphere, and Poseidon Select models.
  • Membrane
    E-chips and other MEMS devices that in closed cells need very thin sample supports that confine liquids and gasses and remain transparent to the electron beam. Amorphous Silicon Nitride (SiN) about 30 nm thick would be membrane support.

High-Angle Annular Dark Field Imaging (HAADF)

Often known as Z-contrast, this imaging mode in STEM uses electrons strongly scattered by the electron beam. The brightness of the preceding image correlates to the atomic weight of the element.


In situ microscopy lets researchers see processes happening in real time, which is extremely important. In situ microscopy has already opened the doors for innovative experimental design, new types of research possibilities, and influential conclusions. As technology continues to develop, there will no doubt be even more scientific breakthroughs using in situ in the future.

This information has been sourced, reviewed and adapted from materials provided by Protochips.

For more information on this source, please visit Protochips.


Please use one of the following formats to cite this article in your essay, paper or report:

  • APA

    Protochips. (2018, October 25). Important Terms for In Situ Microscopy. AZoNano. Retrieved on June 24, 2019 from

  • MLA

    Protochips. "Important Terms for In Situ Microscopy". AZoNano. 24 June 2019. <>.

  • Chicago

    Protochips. "Important Terms for In Situ Microscopy". AZoNano. (accessed June 24, 2019).

  • Harvard

    Protochips. 2018. Important Terms for In Situ Microscopy. AZoNano, viewed 24 June 2019,

Ask A Question

Do you have a question you'd like to ask regarding this article?

Leave your feedback