Protocol Basics

A Protocol is a JSON measurement procedure sent by a PhotosynQ application to an instrument. It defines actions such as sensor reads, light pulses, timing, repeats, and environmental measurements. The instrument runs those instructions and returns raw measurement data to the application.

A Macro is optional analysis code associated with a Protocol. After the measurement returns, the application runs the Macro to calculate named outputs, warnings, and traces for review.

How a Measurement Works

1. Select a Protocol that supports the intended instrument and firmware.
2. The Android or desktop application sends the Protocol to the MultispeQ.
3. The MultispeQ v2.5 runs the measurement and returns raw data.
4. The application runs the associated Macro when one is available.
5. Review calculated outputs, warnings, and traces before saving or repeating the measurement.

MultispeQ v2.5 used for Protocol measurements

Compatibility first

Confirm the supported instrument model, firmware, sensors, optical channels, and calibration requirements before field collection. Test the exact Protocol and Macro with the intended MultispeQ configuration.

Protocols in Projects

A Project Protocol gives contributors one defined measurement procedure. Select it while creating or editing the Project, then test the complete Project workflow before collection.

Current web Project Protocol selection

Project Questions provide the sample and treatment metadata associated with each measurement. They do not change the instrument instructions unless the Protocol explicitly uses supplied variables.

Android Application

Use Quick Measurement to run an available Protocol locally without contributing the result to a Project.

1. Open Quick Measurement from the main menu.
2. Select a compatible Protocol.
3. Position the instrument or sample as required by the Protocol.
4. Keep the MultispeQ steady until the measurement finishes.
5. Review the outputs and quality messages provided by the selected Protocol and Macro. Open trace views when they are available.

Select a Protocol	Review the Result

Quick Measurements are not Project contributions and cannot be uploaded as Project data. A result may remain in the local Measurements history for review. For structured research collection, open the Project and use Take a Measurement so the result is saved with its Project Questions and other metadata.

Desktop Application

The desktop application supports running Protocols, bench measurements, local Notebook workflows, and Protocol or Macro development. The editor can be reviewed without an instrument; connect the intended MultispeQ before running instrument code.

1. Open Protocols to select and run an available Protocol.
2. Open Editor to create or inspect Protocol and Macro code.
3. Use Protocol Code for instrument JSON and Macro Code for result-processing JavaScript.
4. Load a representative saved measurement when testing Macro output.
5. Connect the intended MultispeQ by USB or supported Bluetooth serial connection before running the Protocol.
6. Use the Output, Functions, Variables, and Measurement views to inspect the complete workflow.

Current Desktop Macro Code workspace before loading a measurement

Editing a Protocol or Macro can change the scientific meaning and comparability of its outputs. Save a new version, document the change, and do not silently replace the method during an active study.

Preset and Account Protocols

PhotosynQ preset Protocols are marked with a star where supported. Other Protocol availability depends on the signed-in account, Project, and application context.

Before choosing a Protocol, review:

• Measurement purpose and expected outputs
• Supported MultispeQ model and minimum firmware
• Required sensors, LEDs, detectors, and calibration data
• Sample positioning and environmental requirements
• Connected Macro and warning behavior
• Approximate measurement duration

Incompatible Protocols

An incompatible Protocol can fail to start, return incomplete or misleading data, trigger unintended optical channels, or require an instrument restart. If a test fails:

1. Stop collection.
2. Restart and reconnect the MultispeQ if needed.
3. Confirm the instrument version, firmware, and calibration memory.
4. Review the Protocol requirements and application logs.
5. Retest with a known-good sample before resuming collection.

Do not change a Project Protocol after collection begins without a documented amendment and a plan for handling comparability between versions.