Bartosz Marzec CryoEM · software · systems

Cryo-electron microscopy · automation · instrumentation

Making complex microscopy workflows work in the real world.

I’m Dr Bartosz Marzec, a scientist and engineer working where advanced electron microscopy meets software. I design practical systems that make demanding experiments clearer, safer and more reproducible.

Explore my work Start a conversation
  • High-End TEM & Applications Specialist
  • JEOL Group
  • Supporting laboratories internationally
Dr Bartosz Marzec
Current focus CryoEM workflows & instrument automation
Microscope control SerialEM integration Scientific software Cryo-electron tomography Training & applications

Profile / 01

Science, engineering and the realities of the laboratory.

I translate complex instrument behaviour into workflows people can understand, maintain and trust.

My work sits at the intersection of electron microscopy, scientific instrumentation and software development.

As a High-End Instrument Specialist at JEOL, I support instruments and customers through commissioning, alignment, training and demanding experiments. Alongside that work, I develop prototypes, workflow helpers and educational tools that contribute to the JEOL ecosystem.

These tools grow from close collaboration with laboratories across Europe, the UK, the United States, China and Japan. The aim is simple: remove avoidable friction while keeping advanced workflows transparent and reproducible.

Approach Root cause before workaround.

Listen carefully, diagnose the system, then reduce complexity.

Toolbox Python · PyJEM · C++ · Qt

Software that interfaces directly with instruments and acquisition systems.

Perspective Academia → facility → industry

A view shaped by research, multi-user operations and applications support.

Selected systems / 02

Tools built around how microscopes are actually used.

Four projects exploring deeper control, safer automation and more useful feedback for high-end JEOL TEM workflows.

Active developmentSerialEM · JEOL TemExt

SerialEM JEOL TemExt Plugin

A deep integration layer that brings JEOL’s microscope control interface directly into SerialEM, enabling event-driven automation beyond generic cross-vendor controls.

  • Instrument control
  • Event-driven scripts
  • CryoARM workflows
  • Safety monitoring
Technical overview

SerialEM is an open, community-driven platform for microscope control and automated acquisition. Because it supports many microscope families, its common interface necessarily focuses on functions shared across platforms. The JEOL TemExt Plugin opens the wider JEOL control stack to that ecosystem.

Through the TEM External API, scripts can access the electron gun and emission, condenser system, apertures and deflectors, objective and projector lenses, stage, vacuum status and energy-filter parameters. On CryoARM instruments, the interface also covers autoloader control, sample inventory, liquid-nitrogen monitoring and cryogenic safety interlocks.

Its event-driven architecture forwards internal microscope events into SerialEM as structured signals. Scripts can react to high-tension changes, magnification switches, stage movement, refill status and vacuum transitions without fragile polling loops.

Plugin, manual and example scripts
02 Virtual TemCon control interface Remote control & AFIS
C++ / QtRemote operation

Virtual TemCon

A virtual microscope console for complete keyboard-and-mouse operation, with advanced aberration-free image shift for arbitrary positions on the specimen.

  • Virtual hand panels
  • Free AFIS
  • Remote workflows
  • SerialEM API
Technical overview

Virtual TemCon began during the COVID-19 pandemic as a way to operate JEOL microscopes without physical hand panels. It remains useful for remote work, training and high-throughput CryoEM data collection.

Beyond beam, stage, focus and magnification control, VTC provides live aberration-free image shift for arbitrary specimen positions. This “free AFIS” approach is useful for tomography lamellae, heterogeneous targets and non-standard supports—not only regular single-particle grids.

Because it connects directly to JEOL controls, compensation can use several deflector systems rather than standard beam-shift coils alone. SerialEM scripts and Python modules can call calibration, compensation and movement functions directly.

See an AFIS-enabled study
03 Shepherd beam diagnostics and alignment interface Beam diagnostics
GPU acceleratedAlignment engine

Shepherd

A quantitative beam-diagnostics and auto-alignment engine designed to make routine microscope alignment faster, more consistent and less dependent on subjective visual judgement.

  • OpenCV / OpenCL
  • Live beam metrics
  • Auto-alignment
  • TCP control
Technical overview

Shepherd connects to JEOL TEM External for control and TEM Detector Service for live fluorescent-screen images. A C++/Qt/OpenCV/OpenCL pipeline filters each image, enhances its edges and fits an ellipse to reconstruct a robust model of the beam footprint.

The model provides beam position, deviation from screen centre, area, average diameter, circularity and integrated intensity. Those measurements support automatic gun-shift, condenser-aperture and condenser-astigmatism alignment, with further beam-shift and beam-tilt compensator routines under development.

A built-in TCP server lets SerialEM scripts or external Python tools invoke Shepherd’s camera, diagnostic and alignment functions as part of larger automated workflows.

04 EM Reporter mobile monitoring interface Remote monitoring
ExperimentalCross-platform

EM Reporter

A secure web concept for checking microscope state, receiving threshold alerts and, where site policy allows, performing a small set of controlled remote actions.

  • Web push
  • Regional hosting
  • TLS 1.3
  • Open API
Technical overview

EM Reporter grew from an internal mobile tool for service engineers and users. Its browser portal can show liquid-nitrogen levels, emission current and configured alerts on desktop and mobile devices, without a full remote desktop session.

The microscope-side Python client connects through TEM3 getters and the EuroPyJEM event layer, while the server uses Python, JavaScript and PostgreSQL. Regional instances are designed to keep microscope and user data inside the appropriate jurisdiction.

Remote operations are intentionally subject to local administration and safety policy. The open API also makes it possible to send custom notifications from SerialEM scripts or integrate microscope events into higher-level workflows.

Open the prototype

Career / 03

A path from materials chemistry to high-end TEM systems.

Each stage added a different lens: synthesis, structural analysis, biological mineralisation, facility operations and international applications support.

  1. Foundation

    Cracow University of Technology

    MSc in Chemical Technology, specialising in polymer technology. Research on microwave-assisted poly(aspartic acid) synthesis established an early focus on process optimisation and reproducibility.

  2. Doctoral research

    Trinity College Dublin

    PhD in Inorganic Chemistry with Prof. Wolfgang Schmitt, studying coordination networks and their transformation into inorganic phases. SEM and TEM became central tools for structural analysis.

  3. Postdoctoral research

    University of Leeds

    With Prof. Fiona Meldrum, investigated single-crystal composites and the pathway from organic additive binding to occlusion within inorganic crystals.

  4. CryoEM & tomography

    University of Edinburgh

    With Dr Fabio Nudelman, developed end-to-end cryo-electron microscopy and tomography workflows to study coccolith formation in marine algae.

  5. 2018–2019

    Research Complex at Harwell · UKRI MRC

    As an Electron Microscopy Specialist, shifted focus toward the reliability, operation and optimisation of a multi-user microscopy facility.

  6. 2019–present

    JEOL Group

    High-End TEM and Applications Specialist supporting advanced cryoTEM installations, commissioning instruments, configuring acquisition environments, training users and developing automation tools.

Research / 04

Selected publications.

Work spanning biomineralisation, cryo-electron tomography, crystal growth, composite materials and microscopy-led structural analysis.

17 selected publications

2024

Dystrophic calcinosis: structural and morphological composition, and evaluation of EDTA for potential local treatment

Phillip Lee, Lorraine Green, Bartosz Marzec, Fiona Meldrum, Francesco Del Galdo, Begonya Alcacer-Pitarch

Arthritis Research & Therapy, 26(1), 102

↗
2022

Micron-sized biogenic and synthetic hollow mineral spheres occlude additives within single crystals

B. Marzec, J. Walker, Y. Jhons, F. C. Meldrum, M. Shaver, F. Nudelman

Faraday Discussions, 235, 536–550

↗
2021

Dichroic Calcite Reveals the Pathway from Additive Binding to Occlusion

D. C. Green, R. Darkins, B. Marzec, M. Holden, B. Kahr, D. M. Duffy, F. Meldrum

Crystal Growth & Design, 21(7), 3746–3755

↗
2020

Disordered Filaments Mediate the Fibrillogenesis of Type I Collagen in Solution

A. R. McCluskey, K. S. W. Hung, B. Marzec, J. O. Sindt, N. A. J. M. Sommerdijk, P. J. Camp, F. Nudelman

Biomacromolecules, 21(9), 3631–3643

↗
2020

Morphological development of Pleurochrysis carterae coccoliths examined by cryo-electron tomography

J. M. Walker, B. Marzec, N. Ozaki, D. Clare, F. Nudelman

Journal of Structural Biology, 210(1), 107476

↗
2019

Three-dimensional architecture and surface functionality of coccolith base plates

B. Marzec, J. M. Walker, M. Panagopoulou, Y. Jhons, D. Clare, A. Wheeler, M. P. Shaver, F. Nudelman

Journal of Structural Biology, 208(2), 127–136

↗
2019

Polymorph Selectivity of Coccolith-Associated Polysaccharides from Gephyrocapsa oceanica on Calcium Carbonate Formation In Vitro

J. M. Walker, B. Marzec, R. B. Y. Lee, K. Vodrazkova, S. J. Day, C. C. Tang, R. E. M. Rickaby, F. Nudelman

Advanced Functional Materials, 29(1), 1807168

↗
2019

β-Chitin Nanofibril Self-Assembly in Aqueous Environments

D. Montroni, B. Marzec, F. Valle, F. Nudelman, G. Falini

Biomacromolecules, 20(6), 2421–2429

↗
2018

Amino Acid-Assisted Incorporation of Dye Molecules within Calcite Crystals

B. Marzec, D. C. Green, M. A. Holden, A. S. Coté, J. Ihli, S. Khalid, A. Kulak, D. Walker, C. Tang, D. M. Duffy, Y.-Y. Kim, F. C. Meldrum

Angewandte Chemie International Edition, 57, 8623–8628

↗
2017

Solid-state transformation of amorphous calcium carbonate to aragonite captured by cryoTEM

J. Walker, B. Marzec, F. Nudelman

Angewandte Chemie International Edition, 56, 1–5

↗
2017

Biomineralization of a titanium-modified hydroxyapatite semiconductor on conductive wool fibres

A. Adamiano, N. Sangiorgi, S. Sprio, A. Ruffini, M. Sandri, A. Sanson, P. Gras, D. Grossin, C. François, K. Chatzipanagis, M. Bilton, B. Marzec, A. Varesano, F. Meldrum, R. Kroger, A. Tampieri

Journal of Materials Chemistry B, 5, 7608–7621

↗
2017

Formation of fluorohydroxyapatite with Silver Diamine Fluoride

M. L. Mei, F. Nudelman, B. Marzec, J. M. Walker, E. C. M. Lo, A. W. Walls, C. H. Chu

Journal of Dental Research, 96(10), 1122–1128

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2017

Bio-inspired synthetic approaches: From hierarchical, hybrid supramolecular assemblies to CaCO3-based microspheres

B. Marzec, L. Zhang, N. Zhu, W. Schmitt

Dalton Transactions, 46, 6456–6463

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2016

3D visualization of additive occlusion and tunable full-spectrum fluorescence in calcite

D. Green, J. Ihli, P. D. Thornton, M. A. Holden, B. Marzec, Y.-Y. Kim, A. N. Kulak, M. A. Levenstein, C. Tang, C. Lynch, S. E. D. Webb, C. J. Tynan, F. C. Meldrum

Nature Communications, 13524

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2014

Homologous size-extension of hybrid vanadate capsules — solid state structures, solution stability and surface deposition

M. B. Mahimaidoss, S. A. Krasnikov, L. Reck, C. I. Onet, J. M. Breen, N. Zhu, B. Marzec, I. V. Shvets, W. Schmitt

Chemical Communications, 50, 2265–2267

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2013

Implementing a Multidisciplinary Program for Developing Learning, Communication, and Team-Working Skills in Second-Year Undergraduate Chemistry Students

N. B. McGoldrick, B. Marzec, P. N. Scully, S. M. Draper

Journal of Chemical Education, 90(3), 338–344

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2013

A facile “bottom-up” approach to prepare free-standing nano-films based on manganese coordination clusters

L. Zhang, C. I. Onet, R. Clérac, M. Rouzières, B. Marzec, M. Boese, M. Venkatesan, W. Schmitt

Chemical Communications, 49, 7400–7402

↗

Application notes / 05

Practical field notes.

Concise, experience-led notes for people working with CryoEM instruments and automated acquisition. The emphasis is on decisions that improve reliability—not generic product documentation.

01 Calibration-free beam centring in SerialEM using the JEOL TemExt PluginTwo CLA1 perturbations, one local response matrix, one correction — no stored beam-shift calibration.
02 Diagnosing acquisition driftIn preparation
03 Safer microscope automationIn preparation

Contact / 06

Interested in microscopy, automation or better laboratory practice?

I’m always happy to exchange ideas about advanced TEM workflows and the practical realities behind them.

b.marzec@jeol.fr