Applied and Integrated Photonics

This year marked the second edition of the workshop on Advanced Imaging and Analytical Methods for Characterization of Microorganisms and Plants, which took place in Kácov on September 30 and October 1.

The scientific program covered a broad spectrum of cutting-edge topics, primarily focusing on Raman spectroscopy and hyperspectral and multispectral imaging. The discussions also extended to complementary analytical techniques, including atomic force and scanning electron microscopy, infrared spectroscopy, mass spectrometry, and advanced microchip fabrication.

The workshop successfully brought together experts from various universities, research institutes, scientific centers, and the industrial sector across the Czech Republic, who shared their latest insights and experience in this rapidly developing field.

The workshop was held with the support of the Czech Academy of Sciences Strategy AV21 – Sustainable food production and consumption.

Our colleague, Ing. Marketa Khyrova, was selected to participate in the 14th Bio-SPM Summer School, organized by the Nano Life Science Institute (WPI-NanoLSI) at Kanazawa University, Japan.

During the intensive five-day program, she worked with Bio-SPM techniques, focusing on the use of AFM to study bacterial cells. The program combined lectures with hands-on experiments conducted under the guidance of NanoLSI researchers, giving participants the opportunity to apply the methods directly in the laboratory. The program gave her the opportunity to deepen her knowledge of AFM, develop new practical skills, and gain experience with experimental work in an international research environment. At the end of the summer school, she presented the results of her project during the final Results Presentation Meeting.

Our PhD student Marketa Khyrova attended the AFM & SPM Meeting 2026 in Leeds, UK, held from June 23 to 25. During the event, she presented a very interesting poster titled "Characterization of bacteria biolayers producing polyhydroxybutyrate", showcasing her research to the international scanning probe microscopy community. More details can be found on the event website: https://www.rms.org.uk/rms-event-calendar/2026-events/afm-spm-meeting-2026.html

Ondrej Vaculik, the group's most recently graduated PhD, attended the BioSpec Summer School at the Norwegian University of Life Sciences (NMBU). The program covered spectroscopy and data science for biophotonics, with hands-on work processing FTIR, HPLC and gas chromatography data using the Quasar interactive coding platform. More details are available on the BioSpec course page: https://www.nmbu.no/en/course/FYS402?semester=2026-H%C3%98ST-2027-V%C3%85R

We are pleased to announce that our Hyperspectral Imaging (HSI) method has been officially integrated into the portfolio of services we offer as a core facility within the Czech-BioImaging national research infrastructure. Czech-BioImaging provides open access to cutting-edge biological and medical imaging technologies for both academic and industrial researchers. By adding HSI to our listed methods at the Institute of Scientific Instruments (ISI CAS), scientists from various fields can now utilize this advanced technology—which combines traditional imaging with spectroscopy to capture hundreds of spectral bands—through the Czech-BioImaging open access framework.

The workshop Advanced Imaging and Analytical Methods for the Characterization of Microorganisms and Plants was held in Dalešice on October 21–22, 2025, under the Strategy AV21 – Sustainable food production and consumption.

The main topics included Raman spectroscopy, hyperspectral and multispectral imaging, as well as other techniques such as atomic force microscopy, scanning electron microscopy, infrared spectroscopy, microchip fabrication, and mass spectrometry.

The workshop successfully brought together experts from various universities, research institutes, scientific centers, and the industrial sector across the Czech Republic, who shared their latest insights and experience in this rapidly developing field.

Between October 15 and 17, 2025, our colleague Ing. Jakub Vejrosta took part in the international conference NANOCON 2025 held in Brno, where he won first place in the Best Poster Award competition.

His presented work, Active Bacterial Orientation for New Generation Biodevices, introduces progress in the active orientation of bacteria using acoustic waves. The research aims at developing biodegradable piezoelectric materials for advanced biosensing and biomedical applications.

Between September 23 and 25, 2025, our team visited the Leibniz Institute of Surface Engineering (IOM) in Leipzig.

As part of the visit, Dr. Mojmír Šerý gave a talk entitled Advanced Spectral Methods and Instrument Design for Measurement of Microorganisms.

We greatly appreciate the warm welcome and the opportunity for fruitful scientific exchange.

We are proud to announce that a collaborative work by researchers from our institute was featured on the cover of the latest issue of Journal of Vacuum Science & Technology B (JVST B), May/June 2025, Volume 43, Number 3.

The cover image, captured during plasma diagnostics experiments, is credited to Lukáš Šilhan, Jon Ander Arregi, Tomáš Plichta, Ondřej Vaculík, Jan Novotný, and Mojmír Šerý.

The corresponding article is available in JVST B 43(3) and can be accessed via DOI: 10.1116/6.0004296.

Congratulations to all authors for this achievement!

On May 5, 2025, we had the pleasure of welcoming a team of distinguished researchers from the Leibniz Institute of Surface Engineering (IOM), Leipzig, led by group leader Dr. Klaus Zimmer, for a scientific seminar held in the lecture hall of our Institute.

The visit was part of a growing collaboration, as our colleague Lukáš Šilhan recently completed a research stay at IOM, where he gained valuable experience and established close scientific connections. This beneficial visit, which extended over several days, culminated in the joint preparation of a project proposal between the two Institutes.

The seminar featured two expert talks:

• Dr. Pierre Lorenz: "Atmospheric pressure pattern transfer by laser and plasma: benefits and problems"
• Dr. Martin Ehrhardt: "Laser-Induced Microplasma in Reactive Atmospheres – a Tool for Precision Etching"

We sincerely thank our guests for their inspiring presentations and the productive scientific exchange that followed.

On February 19, 2025, our Institute had the pleasure of welcoming Assoc. Prof. RNDr. Karel Žídek, Ph.D., from TOPTEC – Research Centre for Special Optics and Optoelectronic Systems, a division of the Institute of Plasma Physics (IPP) of the Czech Academy of Sciences. Together with his colleagues, Dr. Žídek visited our research group and toured several of our laboratories.

During the visit, he also gave an inspiring talk titled:
"Characterization of thin films: what can femtosecond pulses tell us about them?"

We thank Dr. Žídek and his team for an engaging visit and valuable scientific exchange.