LIMS

Colibri helps deliver your microscopy data where it needs to go.

Modern TEM and in-situ microscopy experiments produce far more than images.

A single experiment can include microscope settings, image sequences, detector data, spectrometer data, temperature, pressure, gas flow, liquid flow, electrical bias, current, voltage, sample holder status, timestamps, user notes, sample history, and facility context.

If those pieces are disconnected, the experiment becomes harder to search, harder to reproduce, harder to share, harder to analyze, and harder to trust.Colibri is designed to solve that problem at the source.Colibri is not a LIMS.
Colibri is not an ELN.

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Colibri is not a closed data-management system.Colibri is the open platform layer that helps collect synchronized TEM and in-situ experiment data, preserve the metadata that gives it meaning, and deliver that data to the workflow the customer chooses.

What does a LIMS do?

A Laboratory Information Management System, or LIMS, helps laboratories manage samples, experiments, users, workflows, data records, metadata, storage, retrieval, reporting, compliance, and long-term data access.

In research environments, LIMS platforms often overlap with electronic lab notebooks, scientific data management systems, institutional repositories, cloud storage, local servers, facility scheduling systems, and publication workflows.The goal is simple:Turn experimental output into organized, searchable, reusable scientific data.

For microscopy facilities, this is especially important because data rarely comes from one source. TEM and STEM experiments often combine the microscope, camera, detector, spectrometer, in-situ holder, environmental controller, sample history, user notes, and downstream analysis tools.

When those data streams are not connected, researchers are forced to reconstruct the experiment later from filenames, screenshots, notes, memory, and disconnected folders.

That is not a modern workflow.
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That is a data liability.

A microscope accessory should not pretend to be your laboratory’s data-management system.

Modern laboratories already have mature options for managing research data.

Some facilities use commercial LIMS platforms. Some use electronic lab notebooks. Some use institutional repositories, local servers, cloud systems, or custom research-data infrastructure. Some prefer open-source tools built by national laboratories, universities, and scientific software communities. Many use a combination of all of these.

Customers should not have to abandon those systems just because they need to collect in-situ TEM data.

A microscope accessory should not become another closed software island. When an instrument vendor tries to control the entire workflow from acquisition through storage, analysis, and data management, the customer becomes dependent on that vendor’s hardware, file formats, roadmap, licensing model, and willingness to integrate with the tools the laboratory already uses.

Colibri is designed around a different philosophy.

Customer choice comes first.

Colibri makes TEM data LIMS-ready.

The role of Colibri is to collect the experiment correctly at the source.

That means preserving the relationship between image data, microscope metadata, holder conditions, environmental parameters, timestamps, sample context, user notes, and downstream export paths.

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For an in-situ TEM experiment, that context may include:

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Microscope conditions
Image and detector timestamps
Camera and detector information
Holder status
Temperature
Bias, current, voltage, and resistance
Pressure
Gas flow
Liquid flow
Mechanical or environmental state
Spectrometer or detector data
Sample and experiment identifiers
User notes and facility context
File location and data provenance

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Without this context, the data may still produce an image. But it loses much of its scientific value.

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LIMS-ready TEM data means the experiment is no longer trapped in a folder of disconnected files.

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It means the data is structured enough to search. Documented enough to trust.

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Synchronized enough to compare. Portable enough to export. Open enough to connect. Complete enough to support future analysis, publication, automation, and AI workflows.

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Structured export. API handoff. Direct connectors.

Colibri is designed as a platform for data movement, not software lock-in.

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That platform direction has three parts.

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First, Colibri supports structured export. Experimental data and metadata should be captured in documented, portable formats so customers can move the data into storage, analysis, publication, or archive workflows.

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Second, Colibri supports API-based handoff. Laboratories, OEM environments, institutional repositories, open-source tools, and custom research pipelines should be able to connect to the data without depending on a closed desktop application.

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Third, Colibri can support direct connectors where they make sense. Customers may want data delivered to selected LIMS platforms, ELNs, institutional repositories, cloud storage systems, local servers, OEM microscope environments, Python workflows, open-source microscopy tools, or future AI-ready pipelines.

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The customer decides where the data goes.

Build on what already works.

The scientific community does not need every microscope accessory vendor to reinvent laboratory information management.

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Highly developed commercial LIMS platforms already exist. Open-source systems already exist. National laboratories and standards organizations have already invested deeply in research-data infrastructure, metadata, FAIR data practices, materials data curation, and microscopy experiment records.

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The better path is to build with that ecosystem, not against it.

Colibri is designed to support that direction by focusing on the acquisition and handoff layer:

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Better data in.

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Better metadata with it.

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Better freedom after acquisition.

Customer-owned workflows

Hummingbird Scientific believes customers should own their experimental workflows.

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That means a laboratory should be free to use the LIMS, ELN, repository, OEM software, open-source tool, cloud system, local server, or analysis environment that works best for its research.

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Colibri helps make that possible by collecting synchronized, metadata-rich TEM data and delivering it where it needs to go.

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Not software lock-in. Not another data island. Not a closed workflow pretending to be a laboratory platform.

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LIMS-ready TEM data.

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Customer-owned workflows.

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Open handoff to the tools that matter.

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Research Data Infrastructure References

NIST NexusLIMS

https://pages.nist.gov/NexusLIMS/
Backend LIMS that automatically harvests microscopy data and builds structured XML experiment records.

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NIST NexusLIMS-CDCS

https://github.com/usnistgov/NexusLIMS-CDCS
Front-end interface (based on CDCS) used to access, browse, and manage NexusLIMS XML experiment records.

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NIST MDCS (Materials Data Curation System)

https://www.nist.gov/programs-projects/materials-data-curation-system
XML-based platform for structured materials data curation, transformation, and sharing.

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NIST CDCS (Configurable Data Curation System)

https://www.nist.gov/programs-projects/configurable-data-curation-system-cdcs
General-purpose, FAIR-oriented data curation platform supporting schemas, interoperability, APIs, and modular systems.

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NIST Research Data Framework (RDaF) 2.0

https://www.nist.gov/publications/nist-research-data-framework-rdaf-version-20
Customizable framework for building research data management strategies across the data lifecycle.

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NIST Materials Resource Registry (MRR / NMRR)

https://www.nist.gov/programs-projects/nist-materials-resource-registry
Registry for discovering materials data resources, with metadata, interoperability, and API/web-service concepts.

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MaRDA FAIR Materials Microscopy & LIMS Recommendations

https://www.nist.gov/publications/marda-fair-materials-microscopy-and-lims-data-working-groups-community-recommendations

Community best-practice recommendations for FAIR microscopy data, metadata standards, and LIMS usage.

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4CeeD (Timely & Trusted Curation and Coordination)

https://4ceed.github.io/
Open-source ecosystem for uploading, extracting, organizing, and curating scientific data and metadata.

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Holder Control Software

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Header

Colibri helps deliver your microscopy data where it needs to go.

What does a LIMS do?

A microscope accessory should not pretend to be your laboratory’s data-management system.

Colibri makes TEM data LIMS-ready.

Structured export. API handoff. Direct connectors.

Build on what already works.

Customer-owned workflows

Research Data Infrastructure References

NIST NexusLIMS

NIST NexusLIMS-CDCS

NIST MDCS (Materials Data Curation System)

NIST CDCS (Configurable Data Curation System)

NIST Research Data Framework (RDaF) 2.0

NIST Materials Resource Registry (MRR / NMRR)

MaRDA FAIR Materials Microscopy & LIMS Recommendations

4CeeD (Timely & Trusted Curation and Coordination)

Colibri Platform™

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Holder Control Software

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Header

Colibri helps deliver your microscopy data where it needs to go.

What does a LIMS do?

A microscope accessory should not pretend to be your laboratory’s data-management system.

Colibri makes TEM data LIMS-ready.

Structured export. API handoff. Direct connectors.

Build on what already works.

Customer-owned workflows

Research Data Infrastructure References

NIST NexusLIMS

NIST NexusLIMS-CDCS

NIST MDCS (Materials Data Curation System)

NIST CDCS (Configurable Data Curation System)

NIST Research Data Framework (RDaF) 2.0

NIST Materials Resource Registry (MRR / NMRR)

MaRDA FAIR Materials Microscopy & LIMS Recommendations

4CeeD (Timely & Trusted Curation and Coordination)