Capture holder, microscope, timing, and sample-environment metadata. Then export it to the tools you choose.
In-situ microscopy data is more than an image.
Every frame, video, spectrum, diffraction pattern, or dataset is created under specific experimental conditions: temperature, pressure, gas flow, liquid flow, voltage, current, holder position, microscope state, sample environment, timing, and user-defined events.
Colibri Platform™ is designed to preserve that context.
Colibri connects Hummingbird holder data, controller data, timing information, experiment notes, and available microscope session metadata into an exportable experiment record. That record can then be reviewed, shared, archived, or analyzed using the tools the customer chooses.
Colibri is not intended to replace the microscope operating software, the customer’s preferred analysis tools, or the lab’s existing data systems. Its job is to capture the experimental context and make that context usable outside the original acquisition session.
The image shows what happened. The experiment record helps explain why.
The image is only half the experiment.
In-situ microscopy images are most valuable when they remain connected to the conditions that produced them.
Colibri helps preserve this context as an exportable in-situ experiment record that can travel with the data, support later analysis, and improve reproducibility.
A structural change may depend on temperature. A reaction may depend on gas pressure. A growth event may depend on liquid flow. An electrical response may depend on voltage, current, timing, or device state. A drift event may depend on holder position, tilt, heating history, or microscope conditions.
Without that context, the image may be difficult to interpret later.
What is an in-situ experiment record?
An in-situ experiment record is the structured record of what happened to the sample during an experiment: setpoints, measured values, hardware states, timestamps, alarms, notes, and export files.
These records capture experimental data across multiple domains, providing a complete, exportable view of the conditions applied during each experiment.
Open data exports
Hummingbird Scientific believes in exportable, interoperable experiment records. Researchers should be able to review experimental conditions outside the instrument room, connect control logs with microscope image data, share results with collaborators, and preserve metadata in formats that support long-term, reproducible scientific workflows.
Colibri Platform™ data management is built around open data access, not data lock-in, enabling integration with external analysis tools, custom pipelines, and evolving research workflows.
Aligning control data with microscope data
Manual alignment
The user aligns Hummingbird control logs with microscope image timestamps after the experiment. This is the simplest approach and can support many practical workflows when precise synchronization is not required.
Timestamp alignment
Hummingbird logs and microscope files share timestamps, session identifiers, or file references that help connect control data with image data.
Synchronized workflow
Control actions and acquisition steps are coordinated through supported APIs, OEM software pathways, or custom integration. This may be appropriate for advanced automation, high-value experiments, or customer-specific workflows.
Open-source and analysis workflows
Colibri Platform™ data formats are designed to support open-source tools, custom analysis pipelines, and AI-driven microscopy workflows without requiring proprietary environments.
Export temperature/liquid-flow/control log for alignment with image stack.
Export pressure/gas-ratio/heating history for comparison with image/video data.
Export voltage/current/time data for correlation with detector signals.
Export stage/position/stimulus timing to support external data pipelines.
Export tilt/position/environment state to support reconstruction metadata.
Provide structured telemetry for downstream feature detection or adaptive experiments.
Frequently Asked Questions
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