7 ways to unlock benefits of laboratory automation

By Guido Cimoli

Progress from isolated systems to integrated solutions

Many labs already use automation, but few experience its full potential.

That’s because standard off-the-shelf instruments don’t always match the realities of complex workflows. They handle routine steps, but fall short when systems need to work together — when data must flow across platforms, protocols evolve or proprietary assays demand purpose-built hardware.

Customization transforms isolated assay automation into integrated end-to-end solutions, or simply makes it possible to automate assays that standard systems can’t. Instead of forcing workflows into rigid frameworks, tailored solutions flex to support new methods, new scales and new discoveries.

Here are seven ways customization helps unlock the full benefits of laboratory automation.

1. Automate your entire workflow

End-to-end scientific workflows are rarely contained within one instrument. They typically combine liquid handling with additional devices such as incubators, shakers and plate readers, each performing its role effectively but often in isolation. Without the ability to connect these components, teams are forced to patch gaps in automation with manual labor, leading to disconnected data flow and increasing the likelihood of errors.

Custom systems resolve this by integrating diverse instruments, including those from other manufacturers, into complete, coordinated workflows. Using custom drivers and modular architectures to align mechanics, signals and control, complementary devices are linked with liquid handlers and storage solutions. In an NGS workflow, for example, nucleic acid extraction, fragmentation, adapter ligation, amplification and fragment analysis can be integrated into a single continuous process to produce samples ready for sequencing.

By uniting previously fragmented processes into an integrated, end-to-end workflow, labs gain reproducibility, efficiency and a clear path to growth.

2. Lower barriers through user-friendly design

If an automation system is too hard to use, it will never deliver its full potential. Adoption slows, reliance on a small group of experts grows and the full benefits of laboratory automation remain out of reach.

Customization helps overcome this barrier by building ease of use directly into the system. For hardware, this could mean adding pull-out drawers, allowing readers or other devices to be accessed and maintained without dismantling the setup. For software, it includes creating intuitive, customizable interfaces designed for everyday users, making it easier for labs to manage complex workflows without specialist programming skills.

Smart safeguards can also be built in. For example, software can be configured to monitor the remaining volume of critical reagents and prompt users to load a replacement when supplies run low. The system then ensures that every vial is fully used before switching seamlessly to the next, so reagents never run out mid-run and valuable materials are not wasted. Without this kind of tailoring, operators can end up wrestling with engineer-oriented software where even simple adjustments are code-heavy and cumbersome.

By aligning automation with the way scientists actually work and facilitating simpler service and maintenance, customized systems reduce training burden, minimize downtime and make advanced tools accessible to more people in the lab.

3. Create custom modules for proprietary steps

Standard catalogs only go so far. Many scientific workflows include steps that off-the-shelf systems were never designed to handle, such as using labware that isn’t automation-friendly or integrating hazardous-material enclosures. When that happens, labs are forced to rely on improvised workarounds or keep parts of their process manual, driving variability and slowing progress.

Built-to-spec modules remove this barrier by developing hardware tailored to your workflow. That could mean handling fragile or low-volume samples, automating a proprietary preparation step or engineering a function that simply doesn’t exist in commercial products. Because these custom-built components are designed to integrate with broader systems, they slot into workflows as if they were part of the original platform.

In proteomics, custom modules accelerate process development through parallel screening of chromatographic conditions in a miniaturized column format. This approach enables the simultaneous execution of multiple experiments while minimizing resin, sample and reagent consumption. In cell biology, the ability to autoclave entire modules ensures sterility while reducing the time researchers spend on manual cleaning. And in forensics, custom modules can eliminate contamination risks, while additions like on-deck cameras enable visual documentation of sensitive assays.

Custom modules like these turn bottlenecks into automated steps and reduce the need for workarounds. Instead of adapting protocols to what equipment can do, labs can shape automation around their science. That way, even highly specialized assays realize the benefits of laboratory automation: reliability, consistency and efficiency.

4. Safeguard quality with built-in compliance

In regulated environments, automation must comply with strict documentation and control requirements. Cutting corners — or cutting into equipment — can create real risks. For example, attaching a device to a liquid handler by drilling into its housing may seem like a shortcut, but if performed without proper qualification or documentation, it can invalidate certifications and compromise operator safety.

When you work with a qualified automation partner who applies professional engineering standards to every modification, you avoid these pitfalls. Any structural change to your custom solution is properly designed, tested and, where required, followed by re-certification so that instruments remain safe to operate and compliant with local regulations. Formal factory and site acceptance testing (FAT and SAT) provide documented assurance that the delivered system performs exactly as specified.

On the software side, compliance is built in from the start. Features that support 21 CFR Part 11 — including role-based permissions, secure user management and audit trails — can be integrated as needed, ensuring electronic records meet regulatory expectations. This approach gives labs confidence that automation is not only tailored to their workflows, but also managed in a way that supports reproducibility, accountability and compliance.

5. Expand capabilities without starting over

Labs and workflows continually evolve. What begins as a pilot project may scale to thousands of samples per week or shift from a single workflow to a suite of related assays. Off-the-shelf systems often struggle to adapt, forcing labs to replace devices prematurely.

Customized automation makes extensibility part of the design. In some cases, this involves integrating additional devices into a platform that is already in use. Modular designs allow additional instruments, storage units or automation arms to be incorporated without overhauling the whole system. This makes it easier to extend a workflow step by step, whether adding an incubator to increase capacity or integrating a second liquid handler to double throughput.

In other cases, extensibility means planning a future-proof growth strategy from the very beginning. A system may launch with only the modules required for today’s workflow, but with space and design features that make it easy to add capacity and functionality over time.

By supporting progressive growth, custom automation protects your original investment and minimizes disruption. Instead of starting over when requirements change, labs can expand or reconfigure their platform to match demand, ensuring systems keep pace with scientific ambitions and users reap the full benefits of laboratory automation.

6. Keep workflows moving with innovative software

Seamless integration at the data level is equally important for custom automation solutions. Scheduling software manages the complex challenge of balancing timing with resource availability while capturing system-wide data. With dynamic scheduling to adapt when conditions change and event-driven scheduling to trigger automated actions based on real-time data, workflows remain uninterrupted, adaptable and transparent.

One example of event-driven scheduling is crosstalk between instruments. For example, a live-cell imaging reader can use parallel data acquisition and analysis to deliver real-time assay results directly to the liquid handler. This automatically triggers the appropriate next steps, such as initiating an expansion or passaging workflow once a target confluency is reached, reducing the need for manual intervention and boosting walk-away time.

Software can also support fleet-wide oversight across all individual devices. Laboratory insights tools provide usage data and performance trends that help maximize efficiency, optimize uptime and support better resource planning. This helps labs make informed decisions about how their automation systems are used today and how they can scale for tomorrow.

And because modern assay automation platforms connect directly with existing data management systems such as LIMS and ELNs, results are captured seamlessly, ensuring traceability, compliance and confidence in data integrity.

7. Succeed with one accountable partner

When complex workflows are automated by stitching together equipment from multiple vendors, accountability can become blurred. If a problem arises, responsibility for fixing it is often unclear, leading to delays and finger-pointing. Integration projects also take longer when labs must coordinate across several suppliers, each with their own service processes and priorities.

Working with one experienced, technology-agnostic partner capable of delivering both hardware and software helps avoid these complications. Cohesive custom solutions are designed, built and supported under one roof, covering everything from liquid handling platforms and third-party integrations to scheduling software and compliance features. With a single accountable partner, troubleshooting is faster, upgrades are coordinated and long-term service is consistent, making it easier for labs to implement and maintain automation that truly fits.

“Instead of customers having to bounce between five different companies to schedule maintenance, we handle it all. We ensure the right experts are involved and take it off the customer’s plate.” - Victoria Herschel, Applications Manager, Tecan

For labs, this means less time managing vendors and more time focusing on your science. A single point of responsibility ensures that the automation system works as intended, continues to evolve with changing needs and delivers reliable value throughout its lifecycle.

When off-the-shelf doesn’t fit, Labwerx™ delivers

Extraordinary science shouldn’t be limited by rigid systems or fragmented workarounds.

Labwerx™ helps you go further. With decades of experience and over 2,000 custom solutions successfully deployed, Labwerx combines industry-leading engineering, software and scientific expertise to design solutions built to fit your process, your space and your science.

With global and local support and one accountable partner from concept to operation, Labwerx delivers everything from customized workstations to end-to-end robotic work cells — so you can unlock the benefits of laboratory automation and push the boundaries of what’s possible.

You bring the vision and the purpose; we provide the engineering expertise to design and build the systems that make it a reality. Discover what’s possible with Labwerx.