Custom Microscope Software
Custom Microscope and Scientific Imaging Software
Sciotex develops control, acquisition and image processing software for custom microscopes and scientific instruments, from light sheet and adaptive optics systems to laboratory automation and diagnostic imaging. We work side by side with your scientists, from first prototype to commercialization.
Last updated: October 2026 · Sciotex Engineering Team
The Short Answer
What Is Custom Microscope Software?
Custom microscope software controls a microscope’s hardware, from lasers, scanners and stages to cameras, runs and synchronizes its acquisitions, and processes the images, all built around one instrument and its experiments. Commercial microscopes ship with vendor software; custom and research instruments, and systems on their way to becoming products, usually need software built for their hardware. Sciotex has developed more than 30 custom microscope software applications for over 15 research institutions.
Our work goes beyond microscopes. We build data acquisition, processing and control software for scientific instruments, laboratory automation and diagnostic imaging, and help research groups and companies turn lab prototypes into supported products.
What We Build
Scientific Software Development Services
Scientific instruments live or die by their software. We develop the control, timing, acquisition and analysis layers together, so hardware, data and the people running experiments work as one system.
New to light sheet imaging? Read the light sheet microscopy guide.
Find Your Application
Scientific Systems We Develop
Learn more → Building in LabVIEW, FPGA or real-time? See LabVIEW programming and FPGA software.
Proof, Not Theory
Instruments and Imaging Systems We Have Worked On
From microscopes featured in Science and Nature Methods to diagnostic imaging and lab instruments, each system was built with the scientists who use it.
Multiview Light Sheet Microscope
Control software for a microscope with multiple illumination and detection arms, recording high-resolution time series of living samples.
View example →
Adaptive Optics Microscope
LabVIEW control of a custom two-photon microscope that corrects tissue aberrations with a spatial light modulator.
View example →
SLM Phase Pattern Algorithm
GPU-accelerated phase patterns for spatial light modulators, for selective illumination with real-time feedback.
View example →
CellSpotter Cell Detection
Collects, analyzes and archives microscope images of blood samples to detect circulating cancer cells.
View example →
Biaxial Load Tester
Four stepper motors, load cells and camera tracking measure the mechanical properties of biological and synthetic tissue.
View example →
Well Plate Inspection
Software drives an XY stage, images each well and analyzes samples for characteristics of interest.
View example →
Compare Your Options
Vendor Software, Open Source or Custom?
Most labs start with what the microscope came with. The right choice depends on how far your instrument and experiments go beyond it.
| Option | Strengths | Limits | Best for |
|---|---|---|---|
| Vendor microscope software | Ready to use, supported, tuned to the vendor's hardware | Limited to supported devices and built-in experiments | Standard commercial microscopes |
| Open-source acquisition tools | Free, flexible, large user community | Integration, timing and support are up to your team | Labs with in-house programming capacity |
| Custom control software | Built around your hardware, timing and experiment; documented and supported | Requires development time | Custom instruments, new methods, commercialization |
| Hybrid | Vendor or open-source base with custom modules for new hardware or analysis | Must respect the base platform's limits | Extending an existing system |
Swipe the table to see all columns →
Light sheet, confocal or two-photon?
The imaging method shapes what the software must do: how fast it acquires, how it synchronizes hardware and how much data it handles.
| Light sheet | Confocal | Two-photon | |
|---|---|---|---|
| Illumination | A thin sheet from the side | A scanned focused point | A scanned infrared point |
| Speed | Very fast; whole planes per frame | Moderate | Moderate |
| Phototoxicity | Very low | Higher | Low outside the focus |
| Depth | Good; deeper with adaptive optics | Limited in scattering tissue | Deepest in scattering tissue |
| Best for | Live 3D imaging, embryos, organoids, cleared tissue | Fixed and thin samples, slides | Deep imaging in living tissue |
Swipe the table to see all columns →
Sciotex has built software for light sheet, confocal and two-photon systems, including versions with adaptive optics.
For the details, see light sheet vs confocal vs two-photon microscopy.
The Outcome
What Custom Scientific Software Delivers
Our collaborations have led to numerous publications in leading scientific journals. One of our clients received a Nobel Prize during our years of collaboration.
Working With Sciotex
How a Scientific Software Project Works
What to send us
Every instrument is different. These help us understand yours quickly:
- A description of the instrument and the experiments it runs
- The hardware list: cameras, lasers, scanners, stages and DAQ
- Current software and its limitations
- Expected data rates and storage needs
- Timeline and publication or product goals
Why Sciotex
Why Research Institutions Work With Sciotex
We work on projects with scientists at leading research institutions, biotechnology and medical device companies, building software for cutting-edge biomedical imaging, diagnostic data acquisition and laboratory automation.
Trusted by the most innovative organizations
Before You Start
Custom Microscope Software FAQ
What is custom microscope software?
Software built for a specific microscope or instrument: it controls the lasers, scanners, stages and cameras, runs and synchronizes acquisitions, processes and stores the images, and gives scientists an interface designed around their experiments.
Do you work with commercial microscopes or only custom instruments?
Both. We build complete control software for custom and research instruments, and add modules, new hardware support or analysis to existing systems.
What hardware can you integrate?
Scientific cameras including EMCCD and sCMOS, galvanometers and piezo nanopositioners, Pockels cells and acousto-optic modulators, motorized stages, flip mirrors, shutters and filter wheels, spatial light modulators and deformable mirrors, and much more.
What platforms do you develop on?
LabVIEW on PC, FPGA and real-time targets, with GPU, FPGA and CPU vector processing for high-speed image work. We choose the platform that fits the instrument, the timing and the team that will maintain it.
Can you help commercialize a research instrument?
Yes. We have taken instruments from concept to commercialization, including research institution transfer, customization and continued support for users worldwide.
Do you develop software for medical device and diagnostic systems?
Yes. We develop imaging, data acquisition, test and vision inspection software for diagnostic and medical device applications, such as systems that image blood samples to detect circulating cancer cells.
Have your projects led to publications?
Yes. Our collaborations have led to numerous publications, and Sciotex engineers have been co-authors on papers in journals including Science and Nature Methods.
Do we need a support contract?
No. Working with Sciotex does not require a subscription or support contract. Support is available when you need it.
Free Consultation
Discuss Your Microscope or Instrument
Tell us about the instrument, the hardware and the experiments you want to run. An engineer will review it and suggest the best software approach, with no obligation.
Learn the Technology
Related Guides and Articles
Links
© Copyright 2026 by Coleman Technologies, Inc. DBA Sciotex