Journal Open Access

Methods in Microscopy

Editor-in-Chief: Roger Wepf
Edited by: Andreas Thoss and Martin Friedrich

Language: English

First published: January 1, 2024

Publication Frequency: 4 issues per year

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About this journal

The first volume of MiM will be published with two issues. The next volume will have four issues.

Objectives

“Methods in Microscopy” is your gateway to cutting-edge microscopic and nanoscopic techniques. In an era of rapid scientific advancement, we recognize the importance of methodological innovation often overlooked in research. “Methods in Microscopy” offers an Open-Access platform for the peer-reviewed publication of these methods. Our mission is to make these techniques accessible to a wide audience, fostering understanding and accelerating scientific progress among experts and users.

Topics

Optical Microscopy
Fluorescence Microscopy
Super-Resolution Microscopy
(Low- and High Voltage) Electron Microscopy
Correlative Microscopy
Scanning Probe Microscopy
Microscopy combined with Spectroscopy
Image Analysis/Processing
Automated Microscopy Techniques
Software Development
Hardware Development

Article Formats

Research Articles, Review Articles, Letters, Editorials, News, Views

Your Benefits

First journal with a particular focus on methods in microscopy
Methods enjoy a high probability for citations
Co-operation with a leading global society will ensure rapid growth of the journal
Open Access publication with a full CC BY-license ensures widest dissemination of your research
High-quality single-blind review process
Accepted papers will be published online first as DOI-citable, forward-linked articles for quickest possible visibility to the scientific community

Open Access
Structural details of metal-organic frameworks by quantitative X-ray microscopy

October 6, 2025

Xiao-Meng Sui, Vivek Singh, Michal Lahav, Milko E. van der Boom, Vlad Brumfeld

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High-resolution X-ray microscopy was used to study the volumetric details of metal-organic framework (MOF) single crystals formed by coordination bonds between copper nitrate and an organic ligand. The three-dimensional information of individual crystals was visualized with submicron resolution, from the virtual slicing of the crystals. Density is one of the basic material properties, but conventional methods cannot provide high resolution mapping. To gain further information on material properties, quantification of the density inside individual crystal were made. The metal salt precursor was used as a standard. By using the same acquisition and reconstruction parameters for the sample and the standard, a correlation between the X-ray attenuation/intensity inside one crystal and its density was established. This correlation allowed the determination of the amount and the spatial distribution of material inside one MOF crystal. The results could provide guidance for future crystal design.
Open Access
A novel pressurized operando battery cell for laboratory X-ray computed tomography

October 1, 2025

Luca Weckelmann, Krzysztof Dzieciol, Christoph König, Chih-Long Tsai, Anna Windmüller, Luc Raijmakers, Hermann Tempel, Hans Kungl, Rüdiger-A. Eichel

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Battery research relies on microscopy techniques for their microstructure characterizations and operando mechanism investigations. Such techniques include scanning electron microscopy (SEM) or X-ray computed tomography (XCT). The latter one plays a special role due to its ability to visualize a sample or even a whole cell completely in three dimensions. Additionally, imaging is conducted without destructing the investigated sample enabling the possibility of operando measurements. Therefore, XCT advances to a highly valuable method for investigating battery components and interfaces in the pristine, intermediate and post-mortem state or while operating the battery. Despite the evident advantages, XCT of certain battery types such as lithium metal are challenging due to the combination of low and high attenuating materials and air sensitive elements. This work presents the development of a pressurized operando battery cell for laboratory X-ray computed tomography. The developed cell makes the investigation of air sensitive and for XCT challenging battery systems possible. It is resistant to various chemicals and air-tight, thus suitable for different battery types. A dynamic sealing via a metal bellow allows to set and change the stack pressure during operation and after assembly, respectively. The design is optimized for maintaining a high photon flux without neglecting a reliable long-term sealing and practical handling. Initial measurements of a symmetric lithium metal cell with hybrid solid electrolyte demonstrate the capabilities of the developed cell holder.
Open Access
Key considerations for preparing ion-milled lithium metal cross-sectional samples

September 30, 2025

Yulia Trenikhina, Stephen T. Kelly

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Detailed understanding of lithium anode morphology is essential for solid-state battery technology development. Non-optimal interfacial contacts and structural changes during cycling present significant challenges, limiting both battery performance and wide adoption of solid-state batteries. Cross-sectional sample preparation combined with advanced electron microscopy techniques provides essential insights into the internal microstructure and composition of materials, particularly at critical interfaces. Visualizing degradation is crucial for identifying failure mechanisms and optimizing material performance. This paper explores the temperature dependence of ion-polished cross-sections, offers detailed guidelines for lithium cross-section preparation using a Ga+ Focused Ion Beam Scanning Electron Microscope (FIB-SEM) system, and compares the results to cross-sections prepared with an Ar+ ion polisher. We demonstrate that artifacts introduced during lithium cross-sectioning at room temperature can be eliminated by conducting the preparation at cryogenic temperatures of −100 °C or lower, regardless of the type of ions used in the sputtering process. This guidance helps ensure researchers generate quality cross-sections when evaluating this important field.
Open Access
How to image single isolated atoms by using coherent low-energy electrons

September 26, 2025

Tatiana Latychevskaia

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Coherent low-energy electrons have been demonstrated as a practical tool for imaging individual macromolecules and two-dimensional (2D) crystals. Low-energy electrons exhibit unique properties: low radiation damage to biological molecules and high sensitivity to the local potentials. In this study, we outline the conditions at which single isolated charge-free atoms can be imaged by low-energy electron holography. A single atom produces an interference pattern consisting of concentric fringes of finite diameter and of very weak intensity. The diffraction angle θ , determined as the first minimum of the concentric rings interference pattern, exhibits similar dependency on the source-to-sample distance zs as sin θ ∼ 0.3/ zs 1/2 for electrons of different energies (50, 100 and 200 eV) and scattered off different elements (Li, C, and Cs). The results are compared to the recently reported experimental holograms of alkali atoms intercalated into bilayer graphene and adsorbed on top of graphene.
Open Access
Correlative electron and X-ray microscopy: a new lens for sodium-ion battery research

September 26, 2025

Adrian Mikitisin, Heinrich Ditler, Moritz Schütte

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Sodium-ion batteries (SIBs) are emerging as a promising alternative to lithium-ion technology, with the first commercial cells now available. Understanding their structure and degradation mechanisms is crucial for further development. This study presents a correlative approach combining X-ray and electron microscopy to achieve multi-scale imaging of SIB materials. X-ray microscopy enables non-destructive 3D analysis of electrode architecture, while electron microscopy provides high-resolution insights into particle morphology, interfaces, and failure modes. By integrating these techniques, we establish a comprehensive workflow for analyzing structural and chemical changes. Our results offer one of the first in-depth imaging and analysis of commercial SIB materials and provide valuable feedback for material optimization. This correlative methodology sets a new standard for battery research, advancing the development of next-generation sodium-ion energy storage solutions.
Open Access
Advancing materials and life sciences through next-generation X-ray microscopy

September 24, 2025

Silke Christiansen, Joachim Mayer

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Open Access
The Dublin lens: a Cc = 1.0 mm objective lens intended for CryoEM at 100 keV

September 24, 2025

Germano Motta Alves, Theo Andrews, Patrick McBean, Torquil Wells, Mohamed M. El-Gomati, Stephan Burkhalter, Clemens Schulze-Briese, Pietro Zambon, Greg McMullan, Richard Henderson, Christopher J. Russo, Lewys Jones

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We have designed, fabricated and tested a lens with a chromatic aberration coefficient (Cc) of 1.0 mm, a 4.0 mm pole-gap and 2.0 mm bore that is wide enough to accommodate an anti-contamination system and an objective aperture. This lens extends the temporal-coherence envelope of the electron microscope beyond 2 Å, using a low-cost Schottky FEG. We hope that this lens design can be used to improve all 100 keV electron microscopes designed for single-particle electron cryomicroscopy (cryoEM).
Open Access
Microscopic dual-energy computed tomography (microDECT) imaging of animal tissues: the colour of X-rays

September 11, 2025

Stephan Handschuh, Ursula Reichart, Stefan Kummer, Simone Gabner, Bernhard Ruthensteiner, Andy Sombke, Thomas Schwaha, Christian J. Beisser, Patrick Lemell, David Haberthür, Ruslan Hlushchuk, Rudolf Glueckert, Brian D. Metscher, Martin Glösmann

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In this view article, we present potential applications of laboratory-based spectral dual-energy X-ray microtomography imaging for ex vivo animal tissue samples. Technical details on this topic have been reported in previous work, so we focus explicitly on applications here, discussing both dual-energy imaging for the separation of mineralised tissue from one X-ray dense contrast agent, as well as the imaging of samples stained with two X-ray dense contrast agents. Examples are given for a variety of research areas, including preclinical biomedical phenotyping (vasculature, skeletal development), comparative vertebrate morphology, and invertebrate anatomy. Based on the data presented, we conclude that the use of spectral X-ray information can provide new insights into CT datasets. Although using the dual-energy approach initially requires more effort and cost in data acquisition, this additional effort is often worthwhile, as dual-energy datasets allow for more efficient data visualisation, segmentation, and analysis. Until now, software functions for acquisition and processing of dual-energy data have not been implemented in many of the software toolboxes provided by X-ray microtomography vendors with their scanners. We propose that a user-friendly implementation of software tools for acquiring and processing spectral CT data would be a big step towards a wider use of this promising and powerful imaging approach.
Open Access
Operando XCT with fine sampling of discharge process provides new insights into anode’s morphology evolution in a commercial zinc-air battery

September 9, 2025

Krzysztof Dzięcioł, Yasin Emre Durmus, Eunmi Im, Hermann Tempel, Florian Hausen, Rüdiger-A. Eichel

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Fine sampling of the discharge process revealed details of the anode’s morphology evolution in a commercial zinc-air battery. With special software developed for laboratory XCT scanners, it was possible to observe and quantify the evolution of individual particles. An operando sequence consisting of 30 tomograms within 30 h of discharge at a low C-rate, resulted in shape changes small enough for successful quantification. Two morphological descriptors, i.e. equivalent diameter and complexity factor, were used to assess the morphology of the particles. Details on underlying mechanisms are provided, including the shrinking-core concept, dissolution and the newly observed anisotropic shrinkage.
Open Access
Impact of drying on membrane electrode assembly morphology and performance in PEM electrolysis: insights from X-ray tomography and radiography

July 21, 2025

Christine Heume, Maik Plüm, Ali Javed, Krzysztof Dzieciol, Eva Jodat, André Karl, Günter Schmid, Rüdiger-A. Eichel

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Proton exchange membrane electrolysis cells (PEMECs) are a crucial technology for generating “green hydrogen”, a sustainable energy carrier and versatile platform for synthesizing several chemicals. In the life cycle of a PEMEC, various process stages bare risks of accelerated aging, impacting long-term performance. In the stages of transport and storage of water-filled cell assemblies, a common practice in industry, cation contamination or frost can lead to the degradation of the membrane electrode assembly (MEA) even before its operation. Therefore, as an alternative to transporting and storing the MEA in a hydrated state, this work investigates the possibility of drying the MEA within the cell assembly under controlled conditions to prevent such degradation phenomena. Potential drying induced MEA functionality changes were analyzed using in operando methods, focusing on electrical and gas barrier properties. Butler-Volmer kinetics and electrochemical impedance spectroscopy allowed the allocation of potential performance losses to components. Furthermore, in situ and ex situ X-ray computed tomography (XCT) and optical microscopy investigations gave insights into drying-induced morphological changes within the MEA. In total, three distinct morphological changes were observed and consistently identified: membrane swelling, catalyst layer cracking, and reinforcement detachment, with each posing potential limiting factors for the scalability of the controlled drying process. Ultimately, no significant impact on electrical and gas barrier properties was observed, indicating that the drying process and morphological changes did not adversely affect the short-term operation of the PEMEC.
Open Access
High resolution – large field-of-view 3D imaging of fiber-reinforced composites with complex microstructure: stitching of lab-CT scans with single fiber resolution

July 2, 2025

Benedikt Boos, Christoph Queck, Martin Gurka

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A robust, automated workflow for generating high-resolution large field-of-view 3D representations of carbon- and glassfiber reinforced composites with a complex microstructure is presented for three characteristic, very distinct composite specimens with complex fiber architectures: a carbon fiber weave, a unidirectional composite from recycled carbon fiber yarns and an injection molded glass fiber reinforced composite. Overlapping reconstructed images from X-ray computed tomography, taken with a laboratory CT scanner (Zeiss Xradia Versa 520) with a shifted axis of rotation were registered with a rigid transformation, leading to large field of view data sets of approx. 3.1 × 10 10 voxels with a voxel size of 1 µm 3 . Visual assessment of the resulting quality of the images in the overlapping region reveals no artifacts. Exemplarily, the fiber volume content was calculated after segmentation in a selected volume element in the overlapping area. All datasets can be found in separate archives at ZENODO for further use, e.g. for generating digital twins.
Open Access
Momentum and energy resolution

July 2, 2025

Christian Kramberger, Ryosuke Senga, Yung-Chang Lin, Kazu Suenaga, Thomas Pichler

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The energy and momentum transfered in an elastic scattering event from a fast electron to a plasmon are intimately linked. The in-plane ( q 2 D ) and out-of-plane transfered momenta ( q z ) are however fundamentally distinct in a two dimensional sheet. Their different characters manifest in a sign flip of the power law scaling of momentum and energy resolved electron energy loss spectroscopy at the optical limit ( q → 0). While the scattering cross section of a bulk systems diverges, the response of a dielectric sheet fades out. This makes freestanding 2D sheet materials like graphene a showcase to demonstrate momentum and energy resolution.
Open Access
Strengths and limitations of various analytical methods for all-solid state microbatteries

June 20, 2025

Berik Uzakbaiuly, Andre Borchers, Gihoon Cha, Hyoungwon Park, Mustafa Kocademir, Rajkumar Reddy Kolan, Tor Hildebrand, Peter Suter, George Sarau, Silke Christiansen

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In this study, a comprehensive characterization of the commercially available all-solid-state battery (ASSB) was performed using various analytical techniques. SEM and EDX analyses revealed porosity in the Li 1.3 Al 0.3 Ti 1.7 (PO 4 ) 3 (LATP) electrolyte and Li 3 V 2 (PO 4 ) 3 (LVP) electrode, which hinders lithium-ion transport and affects electrochemical performance. ToF-SIMS confirmed a higher lithium concentration in the electrode compared to the electrolyte, while EBSD showed that the Cu current collector has randomly oriented grains, ensuring adequate electrical conductivity. AFM provided insights into surface morphology and potential distribution, confirming the effectiveness of ion polishing in sample preparation. Raman spectroscopy detected LATP electrolyte, indicating its potential use for process monitoring. Additionally, X-ray microscopy (XRM) enabled non-destructive imaging of the battery’s internal structure, although it was limited in resolving electrode and electrolyte layers. These findings contribute to a better understanding of solid-state battery design and highlight the strengths and limitations of various characterization techniques for performance optimization.
Open Access
Two simple ways of making clean nitrogen-doped graphene for TEM studies

June 19, 2025

Ivan Musil, Lennart Rieger, Arkady V. Krasheninnikov, Jannik C. Meyer

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Graphene is the ideal transmission electron microscopy (TEM) support when it comes to imaging, but often offers poor interaction with samples due to its inert nature, making preparation of the TEM samples difficult. Graphitic nitrogen substitutions in graphene could boost its reactivity while simultaneously bringing minimal disturbance to its periodic structure. Here, two straightforward and easy to implement methods are shown for nitrogen doping of graphene that is already freely suspended on a TEM grid. One procedure utilizes a standard plasma cleaner capable of generating radio frequency plasma, for the other a simple direct current glow discharge plasma chamber was built. Successful implantation of graphitic nitrogen was achieved via both methods and verified by high resolution TEM. A series of experiments allowed to find satisfactory conditions for doping, yielding samples where nitrogen substitutions can be found and imaged within otherwise clean areas of graphene. Interaction of an adsorbate with graphitic nitrogen was observed on an atomic level, demonstrating its capability to bind other materials.

Issue 0

Issue 2

Special Issue: AI in Microscopy; Guest editors: Hubert Mantz and Paula Sampaio

Issue 1

Special Issue: FLIM in material and life sciences; Guest Editors: Werner Zuschratter and Uwe Ortmann

Issue 2

Issue 1

Special Issue: Volume Microscopy Across Scales

Methods in Microscopy publishes special and thematic issues focussed on important and emerging topics in the field of study. The journal has established a rigorous process to ensure that any special issue manuscripts follow the same high-quality standards and peer review processes as regular manuscripts. For further information on the journal’s peer review policy please see the "Instructions for Authors".

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Publication language is English. Manuscripts must be written in clear and concise English.
For a regular submission please us our MS word template (docx format). Authors who like to submit in Latex may use the De Gruyter style file.
The Template for Ethical and Legal Declarations is required for submission (needs to be customized by the submitting author on behalf of all others and uploaded as a separate doc-file at the time of the original submission).
MIM is an open access journal. Each article accepted for publication is subject to an article processing charge (APC). The current APC for MIM is € 2,000. In some cases, authors will be eligible for an APC waiver or discount. For further information on MIM’s APC waiver policy please see the MIM APC policy document.
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We are looking forward to receiving your manuscript!

Editor-in-Chief
Roger Wepf, University of Queensland, Australia

Editor
Martin Friedrich, Germany (editor@methodsmicroscopy.org)

Publishing Editor
Andreas Thoss, Germany

Associate Editors
Andrew Leis, University of Melbourne, Australia
Jens Rietdorf, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil

Editorial Board
Li-An Chu, National Tsing Hua University, Hsinchu City, Taiwan
Christian Eggeling, University of Jena, Germany
Julia Fernandez-Rodriguez, University of Gothenburg, Sweden
Eric Hanssen, University of Melbourne, Australia
Heinrich Hörber, University of Ulm, Germany
Jan Huisken, University of Göttingen, Germany　
Vladislav Krzyzanek, The Czech Academy of Sciences, Brno, Czech Republic
Phillipe Leclere, University of Mons, Belgium
Paul McMillan, University of Melbourne, Australia
Kota Miura, Bioimage Analysis & Research, Okayama, Japan
Wiebke Möbius, MPI Göttingen, Germany
Francesco Simone Ruggeri, Wageningen University & Research, The Netherlands
Paula Sampaio, University of Porto, Portugal
Owen Schwartz, NIAID-NIH, Bethesda, Maryland, USA
Erin Tranfield, VIB Bio Imaging Core Ghent, Belgium
Marc van Zandvoort, Maastricht University, The Netherlands
Andreas Walter, University of Aalen, Germany　
Ralf Wolleschensky, Carl Zeiss Microscopy, Jena, Germany
Xiuzhen Yu, RIKEN Center for Emergent Matter Science, Wakō, Japan
Ruobing Zhang, Chinese Academy of Science, Suzhou, China

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Additional information

eISSN:

2942-3899

Language:

English

Publisher:

De Gruyter

Additional information

First published:

January 1, 2024

Publication Frequency:

4 issues per year

eISSN: 2942-3899

Creative Commons

BY 4.0

Methods in Microscopy

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