LIMS Implementation

Tips for SampleManager LIMS Instrument Integration

LIMS Implementation

October 22, 2020

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The following blog will detail SampleManager LIMS Instrument integration best practices and procedures to ensure success.

Technological advances in laboratory instrumentation, along with higher throughput processes, have led to massive increases in the volume of analytical data. One of the main challenges faced by organizations today is turning this vast amount of data into useful information that fuels innovation and enables timely and effective business decisions. In order to manage and process these growing data volumes effectively, laboratories are looking to automate and integrate laboratory operations and processes as much as possible.

Towards this end, integration of laboratory instruments with a LIMS (Laboratory Information Management System) automates laboratory processes and drives operational efficiency by reducing data transcription errors and increasing sample throughput. Instrument integration with LIMS also serves to increase job satisfaction by reducing tedious tasks like manual data entry and writing of results, allowing scientists to spend more time doing the science that leads to innovation. Connecting the information generated by instruments and informatics systems is a key to transforming your laboratory operations, improving product quality, and turning your data into knowledge.

Instruments that are commonly integrated with LIMS in laboratories include:

  • GC
  • GCMS
  • HPLC
  • LCMS
  • ICP
  • Particle Counters
  • DNA Sequencers
  • Balances
  • Titrators
  • AA Analyzers

The latest versions of SampleManager LIMS™ provides a number of effective mechanisms to accomplish instrument integration. In this blog, we will discuss some best practice recommendations when integrating laboratory instruments with SampleManager LIMS™ in order to ensure that your enterprise maximizes success in ensuring compliance, streamlining processes, improving quality, reducing costs, and driving productivity and innovation in your laboratory environment.

Instrument Integration Tips

Triage which instruments are worth integrating

Before you invest the time and effort to integrate an instrument with SampleManager LIMS™, it is important to consider the cost/benefit ratio involved. Implementing an instrument integration can be a time-consuming task – anywhere from a few hours to a several days – so it is advisable to determine if the ROI makes the instrument integration worth pursuing. Some of the factors involved in this analysis are:

  • How frequently is the instrument used and what quantity of results will it export?
  • How critical are the instrument’s results for laboratory processes?
  • Can the instrument’s PC be easily connected to the network so the instrument can be integrated with the LIMS?

For this last point, it is important to consider operating system actualization, network compliance issues such as company IT policies, and the complexity of the data being exported by the instrument.

Go for the Low-Hanging Fruit First

Once you have your list of instruments that make sense to integrate, you’ll want to go for the low-hanging fruit first in order to build project morale and momentum. This means integrating critical path instruments first – those that are relatively straightforward to integrate, high throughput, and add a lot of value to the business.

Laboratories often want instruments such as balances to be integrated due the fact that they are critical to their processes. Balances can be problematic, however, due to a number of factors such as age, connectivity and logistics. An instrument like a GC or HPLC with high throughput and compatible software would probably be a better choice to place at the top of your integration list. Working with a quality informatics consultant that can help you develop an effective roadmap and outline a realistic amount of scope for your project is very important.

Standardize Export Formats

The data exported by instruments either have a fixed format, or can be formatted as the operator desires using exporting templates defined on the instrument software. For this latter case, it is important to configure an export format that is both flexible (allowing all possible instrument methods to work and be imported into the LIMS) and fixed (it does not vary for different methods or different instrument runs). The day-to-day instrument operators should not have the ability to change the export templates. If a different export template is used, parsing scripts developed for the instrument will need to be adjusted to keep it working properly.

SampleManager LIMS™ Instrument Integration Options

Once the decision is made to integrate an instrument with SampleManager LIMS™, the integration method needs to be determined. There are several different ways to integrate instruments with SampleManager LIMS™ which we will describe below.

Serial/RS-232 interface

The functionality required to integrate serial instruments with SampleManager (e.g. balances, pH meters) is built within the system. These instruments usually require a physical cable connection between the instrumentation and the workstation running SampleManager. The COM port parameters can be defined within SampleManager for the instruments.

Different setups/hardware options (Serial Device Servers) can be explored if multiple instruments need to be connected through this serial interface to the same SampleManager workstations; or to make the same instrument available to different SampleManager workstations through the network. Some VGL customization is required for this setup.

Instrument Manager

Also known as SM-IM, or the “SampleManager Instrument Manager” module. The SM-IM module allows SampleManager to read result files from instruments. Virtually any instrument that is networked and can produce a result export in a file format can be integrated with SampleManager using this module.

The SM-IM module utilizes parsing scripts (to parse the important information from a result file), mapping scripts (to map the parsed data to SampleManager entities) and an alias table (to map specific entries between the instrument and SampleManager, like name of analysis methods and results). Each instrument to be integrated will have a parsing script, mapping script and an alias table defined on the SM-IM module. The instrument is then configured to export files to a specific network folder, where SM-IM interface will process the files and send the results to SampleManager (through LIMSML).

This SM-IM module is easy to use and configure. The main limitation is that it is a unidirectional interface, so it won’t allow SampleManager to send data to the instrument (such as list of samples to be analyzed).

New SM12.1 LES Instrument Integration (“New” SM-IM)

Together with the SampleManager LES functionality (standard on SM12.1), Instrument and Workflow functionality were extended to support manual Instrument Integration that is compatible with the SM12+ web client. The Instrument Entity has a tab for configuring Integration properties, which includes the ability to specify a Data Source for the integration.  Data sources can be:

  • Emulated
  • Serial Port
  • Directory
  • Web Request
  • File Prompt

Parsing scripts and Alias table can be defined within SampleManager for the LES Instrument Integration.

Once the test is assigned to an instrument on the SampleManager result entry screen, the system will allow results to be imported based on the Serial/Data Source configuration defined for the instrument. This is a unidirectional (Instrument  SampleManager)  instrument interface mechanism.

The SampleManager Workflow Entity was also extended and has new nodes to streamline instrument integration.

Integration Manager

Integration Manager is a stand-alone Thermo Fisher application/product that allows for bi-directional integration with instruments, services or third-party applications using the concept of integration points. When utilized for instrument integration, Integration Manager can be configured to send SampleManager information to the instrument (usually the list of samples and some sample properties), and to retrieve results back from the instrument (usually exported to files on a network folder). More complex setups with multiple interfaces and multiple integration points can also be used to address very complex integration scenarios.

Integration Manager is a stand-alone product with its own license, user interface and database objects that is designed to work with many different systems, not just SampleManager. Integration Manager acts like a translator of different languages from disparate data sources, accepting and delivering data in the format appropriate to each intended recipient.

When used specifically for SampleManager instrument integration, Integration Manager allows the creation of transformations (similar to parsing and mapping scripts) and alias tables and makes available ‘File Agents’ and ‘SampleManager’ agents to complete the integration.

Chromeleon Link

Specific functionality to integrate SampleManager with Chromeleon (a CDS from Thermo Fisher Scientific) was released with SM 11 and is being continuously enhanced on service releases and newer versions of SampleManager (12 and 12.1).

This interface allows bidirectional communication between SampleManager and Chromeleon, where:

  • SampleManager can send Sequence List to the Chromeleon instrument.
  • SampleManager can import the Sequence information and results seamlessly from the Chromeleon instrument.
  • Chromeleon software can search for Sequence information directly on the SampleManager system (through Batches and Standards Configuration on SampleManager) using Chromeleon e-Workflow wizard.

Custom Instrument Integration

Customers sometimes choose to customize their instrument interfaces (bi-directional from SampleManager –>Instrument and from Instrument –> SampleManager) and do not use any of the tools available from Thermo FisherWhile this allows flexibility, like any other customized solution, it is not sustainable for a long-term strategy and will require a lot of attention as SampleManager evolves and upgrades take place. Usually maintenance costs of custom solutions are very high, so all other options should be exhausted before going down this path.


Whether you have old instruments that were not integrated with SampleManager during your initial implementation, or new instruments that have come online since, a SampleManager upgrade (or a new implementation) is a convenient time to integrate instruments with the system. Effective instrument integration is crucial to improving your organization’s IP protection and SampleManager adoption and utilization rates, and a key factor in enhancing productivity, efficiency, data integrity and innovation in your laboratory environment. Automating your laboratory environment through effective instrument integration, however, is best accomplished through a close partnership with a quality informatics consultant. As a long-standing Thermo Fisher Scientific’s services partner, Astrix is uniquely positioned to help you optimize your SampleManager LIMS™ implementation and instrument integrations.


Contact us today and let’s begin working on a solution for your most complex strategy, technology and staffing challenges.

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