Microscopy software & integrations

Custom software for microscopy workflows that need more than the standard tools allow

Automation, image analysis, guided workflows, hardware integration, and structured reporting for ZEISS-based environments. Built around your actual setup, your constraints, and your way of working.

Project-based: fixed scope, fixed price, with a practical delivery path from first use case to production-ready workflow.

X Y
About SmartLabs

Specialized software engineering for ZEISS-based microscopy environments

SmartLabs is an expert software team working in and around ZEISS-based microscopy environments. We build the missing layer between the instruments' technical capabilities and your specific application requirements.

Most of our work is delivered as custom, project-based software for a specific use case, instrument setup, or operational constraint. Depending on the project, that may mean software inside ZEN, connected components around it, or an integration between the microscope workflow and external tools.

Independent of ZEISS, with seven years of hands-on experience across ZEN Blue, ZEN Black, and ZEN Core, SmartLabs works across research and industrial contexts where repeatability, usability, and maintainability matter.

Industries
Semiconductor Life Science Medical Devices Aerospace Automotive & Manufacturing Materials Research Oil & Gas Academic Research
Experience
7 years in the ZEISS ecosystem
Platforms
ZEN Blue · ZEN Black · ZEN Core
Motorized and non-motorized systems
Widefield · confocal · SEM · slide scanner
Stack
HALCON · MVTec DL · Arivis · Intellesis · QuPath
Python, .NET, OAD / VBA
What we do
01
Workflow automation

Acquisition sequences, tiling, time-lapses, batch runs, and repeatable execution logic built around your specific process.

02
Image analysis & measurement

Detection, segmentation, classification, and measurement pipelines adapted to your sample types and reporting needs.

03
Hardware & software integration

Hardware triggering, external device control, third-party tool and API connections, natively inside the workflow.

04
Export, reporting & traceability

Structured outputs, consistent naming, automated PDF or Excel reports, LIMS and storage handoffs.

05
Operator-facing interfaces

Guided run controls, input forms, and custom ZEN windows that make complex workflows safe for non-expert users.

We support different types of microscopy work

Select the path that best fits your situation.

How a project works
01
Discovery. Understand the workflow and constraints
02
Proposal. Written scope, fixed price
03
Build. Built around your actual setup
04
Handover. Tested, documented, delivered
05
Support. Included after delivery
Selected work

Specific workflow problems we have solved

Examples from real microscopy and imaging workflows.

Aerospace
Automated microstructure assessment for additive manufacturing repair

Deep-learning instance segmentation detects porosity, cracks, and inclusions on turbine alloy coupons, replacing manual metallographic inspection. Operator review step before the final PDF report.

ZEN Core HALCON MVTec DL
Standardised reports across alloy types, with human oversight loop
Semiconductor
Automated wafer defect inspection and density mapping

End-to-end automation of illumination calibration, tile acquisition, threshold segmentation, and OISF density mapping across sectors. Cross-diametrical and full-wafer modes.

PDF report CSV report
45 min–4 h manual inspection → ~10–15 min automated
Medical Devices
SEM fiber thickness measurement for neurovascular implants

Template matching localises fiber regions; instance segmentation measures thickness at sub-pixel precision. Hybrid approach: automation handles detection, operator validates before reporting.

HALCON Arivis Cloud
200–300 fibers per run, in minutes vs. hours
Life Science
Closed-loop root tracking on ZEISS LSM 700

Acquires images at set intervals, estimates root tip displacement via image registration, and repositions the stage to keep a growing root in view through unattended overnight sessions.

ZEN Black VBA macro LSM 700
Continuous multi-hour time-lapses without operator intervention
Industrial
AI weld measurement server inside existing QC software

Semantic segmentation (geometry + defect models) and a measurement library run on a secured intranet server. Results return as JSON overlays directly inside the customer's own application. One button replaces ruler-by-ruler manual work.

HALCON Semantic segmentation JSON overlay
~5 min per image → 15–30 sec per image
Research Instrumentation
Correlative AFM + LSM acquisition without manual synchronisation

Monitors a shared folder for AFM line completion events, then triggers the matching LSM scan, achieving line-by-line synchronisation between two hardware-independent systems without modifying either.

ZEN Blue Experiment Feedback
Correlative datasets without post-hoc manual alignment
FAQ

Common questions

What exactly do you build?
Custom software for ZEISS-based microscopy workflows. In many projects, that means code running inside ZEN Blue, ZEN Black, or ZEN Core: Python scripts, OAD macros, .NET extensions, or a combination. In other cases, the project also includes connected components around ZEN, such as external hardware control, analysis services, reporting, or data handoff to other systems.
How does a project work?
It usually starts with a free discovery call. We understand the workflow, the setup, and what is not working well enough, then come back with a written scope and a fixed price. If the fit is right, we build, test, document, and hand over the software.
Can this be done remotely, or do you need to be on-site?
Most projects can be delivered without us travelling on-site. We do most of the development in local simulations on our own systems, then connect remotely for testing, validation on the real setup, demos, and debugging. That usually requires someone on-site to start the system, prepare the sample, handle the basic setup, and give us access. If confidentiality or project constraints require on-site work, we can do that too.
Will it work on our specific microscope and ZEN version?
That depends on the instrument, the ZEN version, and what the workflow needs to do. During the first conversation, we map what your system supports and tell you clearly what is feasible, what is not, and where the constraints are.
Do you only work with ZEISS systems?
Most of our work involves ZEISS instruments and the ZEN software ecosystem, because that is where our depth of experience is. Some projects extend beyond that, including external hardware integration, server-side processing, or instrument-agnostic analysis pipelines. If you are unsure whether your setup is in scope, describe it and we will tell you honestly.
Are you affiliated with ZEISS?
No. SmartLabs is independent of ZEISS. We are not a ZEISS partner, reseller, or official representative, and we do not present our work as ZEISS-authorized or ZEISS-endorsed. We have seven years of hands-on experience in the ZEN ecosystem, across ZEN Blue, ZEN Black, and ZEN Core, and have worked alongside ZEISS teams on a number of projects.
What happens to the code after delivery?
You receive the delivered code documented and structured for maintenance and extension later, either by your own team or by us if needed. We include a post-delivery support period, and longer-term support can be agreed where useful.
Newsletter

Subscribe to our newsletter

Occasional notes on what we are building: workflow patterns, ZEN automation tips, and lessons from real projects. Roughly once a month, never more. Unsubscribe anytime.

By subscribing you agree to our privacy policy. We use your email only to send the newsletter and you can unsubscribe at any time.

Get in touch

Tell us what you are trying to solve

A rough description is enough. We will come back with honest feedback on what is possible.

Emailoffice@smartlabs.be
First stepA short discovery call. Free, no commitment.
LocationLeuven, Belgium.

By sending this message you agree that we process the information you provide to respond to your enquiry. See our privacy policy.