Environmental electron microscopy
Institute of Scientific Instruments of the CAS, v. v. i.
Detection systems and instrumentation for ESEM

Environmental electron microscopy research group introduction (EEM)

We are pioneers of ESEM (environmental scanning electron microscopy) in the Czech Republic and founders of A-ESEM (advanced environmental scanning electron microscopy). We are a multidisciplinary group of engineers, physicists and chemists, focusing on basic research and applied development in the area of special instrumentation, electron detectors and electron microscopic methods - primarily ESEM/A-ESEM.

The scope of our group covers environmental scanning electron microscopy and the detection of signal electrons, thus continuing in the footsteps of the professor Rudolf Autrata, founder of our research.

Group Profile

Mission and vision

To be world leaders in advanced environmental scanning electron microscopy focusing on static and dynamic in-situ low-dose imaging of weakly emitting samples under conditions of very low electron beam energy and currents. To be among the world leaders in imaging electrically non-conductive wet samples in their native state, which are often sensitive to beam radiation damage. To create new methods, instrumentation and applications for further exploration of the nanoworld.

Advanced environmental scanning electron microscopy
(A-ESEM) beyond the capabilities of commercial instruments.


Advanced environmental scanning electron microscopy

Advanced Environmental Scanning Electron Microscopy (A-ESEM) is a new electron-microscopic method introduced by our group in 2022. It enables material and topographical characterization of electrically non-conductive and partially wet samples using high scanning speeds, low energies and ultra-low currents of the primary electron beam. Samples can be observed in high resolution without the need of plating, freezing and chemical treatment.

Highly moist to liquid samples, samples in their native state and living samples can be physicochemically characterised using the methods we have developed. A-ESEM is suitable for correlative imaging, for example in combination with super-resolution fluorescence light microscopy.

The advantage of A-ESEM is the possibility of static and dynamic in-situ/in-vivo imaging in environmentally relevant conditions. The possibility of working in a pressure range from vacuum to relatively high pressures of various gases gives A-ESEM the greatest application potential of all electron microscopic methods.


A-ESEM possibilities:

Types of working conditions:


Gas pressure from 10-4 Pa to 3 kPa

Electron beam energy from 1 keV to 30 keV

Electron beam current from 0.1 pA to 1 μA

Different types of gases

  • H2O, N2, Ar,......
  • gas mixtures
  • precisely defined relative humidity

Sample temperature

  • from - 60 °C to + 1200 °C
  • from - 190 °C to 0 °C

Types of in-situ experiments:

Micro/nano manipulation

  • Tensile test - Force sensor

Application of chemicals to the sample

  • Gas injection, liquid injection

Diagnostics of sample’s electrical properties

  • EBIC, RCI, EBAC...

Controlled changes in relative humidity

  • Hydration, drying, freezing, melting, sublimation

State/phase changes

  • evaporation, condensation, crystallisation, solidification, melting, (de)sublimation, lyophilization



We study the generation of signal electrons by simulating the interactions of primary and signal electrons with gas, liquid and solid matter.

Using simulations and accurate measurement of thermodynamic parameters in the ESEM/A-ESEM specimen chamber we study gas flow for research and development of new equipment that allows better and more accurate monitoring and control of working conditions in the microscope.

We are developing new, highly sensitive ionisation detectors of signal electrons, scintillation-photomultiplier detectors and advanced instrumentation for ESEM/A-ESEM.

We develop methods to study electrically non-conductive, often moist biological or polymeric samples in the native state, sensitive to radiation damage and dehydration, observed under environmentally compatible conditions of extremely low primary beam energies and currents.

We collaborate with a number of academic partners and companies on the characterization of difficult-to-visualise samples, observed mainly in dynamic conditions – chemical reactions, changes in the morphology of samples due to physical or chemical stimuli and processes.

Detection systems and instrumentation for ESEM
Non-conductive and difficult-to-observe samples
Biological samples
Dynamic in-situ experiments


Our goal is a software that completely predicts the outcome of an experiment. This includes the following areas:

Tracing electrons from their entry into the specimen chamber to their detection.

The exceptionality of ionisation detectors is that signal amplification occurs before detection itself, through electron avalanches in the microscope chamber. Understanding and prediction of their behaviour is thus essential for designing new and improving existing detectors.



doc. Ing. et Ing. Vilém Neděla, Ph.D., DSc.
Senior researcher, group leader
doc. Ing. Jiří Maxa, Ph.D.
Research Fellow
Ing. Jaroslava Bezděková, Ph.D.
Researcher - postdoctoral fellow
Ing. Eva Soukupová, Ph.D.
Researcher - postdoctoral fellow
Ing. Eva Tihlaříková, Ph.D.
Researcher - postdoctoral fellow
Mgr. Ľubica Vetráková, Ph.D.
Researcher - postdoctoral fellow
Mgr. František Martínek
PhD student
Mgr. Martin Olbert
PhD student
Mgr. Kamila Závacká
PhD student
Pavel Vitámvás
Ing. Vladimír Tichý
Ing. Aleš Kondr



A significantly modified high-resolution microscope from Thermo Fisher Scientific (originally FEI). Equipped with special systems developed by the EEM group


  working pressure resolution
SEM mode <6.10-4 Pa

1.2 nm at 30 kV (SED)
2.9 nm at 1 kV (SED)

Low Vacuum mode 10 to 130 Pa

1.4 nm at 30 kV (SED)
3.0 nm at 3 kV (SED)

ESEM mode 10 to 4000 Pa 1.4 nm at 30 kV (SED)



SW Equipment:

Maps + correlative work flow
Digital Surf – Mountains SEM® Expert


EDS Bruker Quantax 400 XFlash 6/100 with almost all SW modules, standard sets, custom libraries and calibrations for A-ESEM



Experimental non-commercial device. Created on the basis of SEM Vega (TESCAN ORSAY HOLDING, a.s.) and rebuilt as part of the dissertation of doc. Neděla


Tungsten thermionic cathode
Acceleration voltage 500 V to 30 kV
1 pA to 2 µA trace current

  working gas resolution
SEM mode <3.10-3 Pa 3.5 nm 30 kV (SED)
ESEM mode 100 to 3000 Pa 10 nm 30kV (BSE)

Microscope equipment:

TESCAN detectors: Scintillation ET SE

ESEM detectors:

Scintillation BSE – right and left detector with the possibility of signal addition and subtraction
Scintillation - ionisation detectors of several types
ISEDS – ionisation detector with electrostatic separator



Imaging thin samples at sub-nanometre resolution
Study of nanoparticles in liquids at nano- to micrometre resolution
Energy dispersive microanalysis including mapping at pressures from
10-3 to 1000 Pa
3D in-situ topography
Spatial display in real time including metrology of the sample surface
Special detection systems
Signal electron detectors developed by us for boundary specific applications
Multimodal correlative microscopy
Correlation with super-resolution fluorescence microscopy, AFM, NMR and other microscopic methods
Physical-chemical research of amorphous ice and frozen solutions
Cooled sample holder
Non-commercial holder with high efficiency and homogeneity of cooling with integrated sensors of thermodynamic parameters
Esternal hydration systems
Sophisticated SW controlled systems for local and global hydration of the A-ESEM specimen chamber

Supporting technologies and methods

  • HW and SW support for particle analysis and metrology
  • Gas flow simulation
  • Heat transfer simulation
  • Electron tracing in gas and solid matter
  • Simulation of electrostatic fields
  • 3D printing
  • Confocal microscopy
  • Fluorescence microscopy
  • Microbiology laboratory
  • Electrochemistry
  • 3D modelling
  • Design and manufacture of electronics
  • Artificial intelligence for data post-processing
  • Image denoising algorithms
  • Automation of microscope control
  • SW development


Academic partners

University of Cambridge (Cambridge, GB)
Charles University (Prague, CZ)
University of Kyoto (Kyoto, JP)
Masaryk University (Brno, CZ)
University of Nagoya (Nagoya, JP)
Institute of Macromolecular Chemistry of the CAS (Prague, CZ)
Wroclaw University of Science and Technology (Wroclaw, PL)
Institute of Biophysics of the CAS (Brno, CZ)
University of technology Sydney (Sydney, AUS)
IKEM, (Prague, CZ)
Technical University of Munich (Munich, DE)
University of Chemical Technology in Prague (Prague, CZ)
British Antarctic Survey (Cambridge, GB)
Brno University of Technology (Brno, CZ)
University of Innsbruck (Innsbruck, AT)
Mendel University in Brno (Brno, CZ)
Aristotle University of Thessaloniki (Thessaloniki, GR)
Institute of Experimental Botany of the CAS (Prague, CZ)


Collaboration with companies

Hitachi High Technologies (Tokyo, JP)
Jeol (Tokyo, JP)
Thermo Fisher Scientific Brno s.r.o. (Brno, CZ)
Tecpa s.r.o. (Brno, CZ)
AutraDet (Brno, CZ)
BVT Technologies, a.s. (Brno, CZ)
Contipro a.s. (Dolní Dobrouč, CZ)
Preciosa a.s. (Jablonec nad Nisou, CZ)
Bosch spol. s.r.o. (České Budějovice, CZ)
NUM solution s.r.o. (Prague, CZ)
Synpo a.s. (Pardubice, CZ)
Agra Group a.s. (Střelské Hoštice, CZ)
Kleindiek Nanotechnik GmbH (Kusterdingen, DE)
point electronic (Halle, DE)
DENSO Manufacturing Czech s.r.o. (Liberec, CZ)
and many others


Environmental Electron Microscopy (EEM) Group
Department of Electron Microscopy

Institute of Scientific Instruments of the Czech Academy of Sciences, v. v. i.

Královopolská 147
612 64 Brno
Česká republika

doc. Ing. et Ing.Vilém Neděla, Ph.D. 
+420 541 514 333  

ID: 68081731
VAT number: CZ68081731