Micro-Manager BeanShell Automation Scripts

A collection of BeanShell scripts for automating microscopy experiments in Micro-Manager, covering stage control (X, Y, Z), camera configuration, image acquisition, and 2D spectral mapping. Written to support real experimental workflows, these scripts are designed as a practical starting point for anyone looking to automate their microscope with Micro-Manager's scripting panel.

Related publication: Optics Express 28(19), 28656 (2020)

Useful API reference: Micro-Manager API for BeanShell

Tip: Navigating Micro-Manager documentation and version compatibility can be tricky. LLMs (Claude, GPT, etc.) are surprisingly useful for debugging BeanShell scripts, as they have good coverage of the MM API.

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Repository Structure

├── MM-1.4/          # Scripts for Micro-Manager 1.4 — stage motion & position lists
└── MM-2.0/
    ├── Basic/       # Camera setup, single acquisition, 2D motor scanning
    ├── Advanced/    # Multi-camera acquisition, spectral mapping workflows
    ├── SpectralMapping-1CAM.bsh      # Full 2D spectral mapping, single camera
    └── SpectralMapping_2CAM.bsh      # Full 2D spectral mapping, dual camera

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MM-1.4 — Stage Motion & Position Lists

Scripts originally developed for system calibration (see paper above). Each script builds a PositionList that can be used with Micro-Manager's MDA (Multi-Dimensional Acquisition).

Script	Description
oneDimensionalStageMotion.bsh	Steps along a single axis (X, Y, or Z) by a fixed step size
twoDimensionalStageMotion.bsh	Steps in a plane (XY, XZ, or YZ) while holding one axis fixed
ArbitraryMotion.bsh	Increments all three axes simultaneously by independent step sizes
3DHelicalStageMotion.bsh	Generates a helical (corkscrew) trajectory in XYZ — used for 3D system calibration
SetCamera.bsh	Configures two DCAM cameras (exposure + ROI) simultaneously

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MM-2.0 — Basic Examples

Foundational scripts for getting up and running with Micro-Manager 2.0's updated API.

Script	Description
CameraSpectraSetup.bsh	Sets up a NIRvana HS camera with exposure and a narrow ROI (for spectrometer slit imaging)
DualCamSetup_Andor_NIRvana.bsh	Configures two cameras (NIRvana HS + Andor) with independent exposure and ROI settings
simple1FrameAcq_datastore.bsh	Snaps a single image and saves it to disk using the MM2.0 Datastore API (RAM → TIFF)
2DStageScanning.bsh	Generates a serpentine (bidirectional) XY position grid and steps through it with the stage

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MM-2.0 — Advanced Examples

More complete acquisition workflows combining stage motion with image capture and saving.

Script	Description
2DScanning&Camera_implementation_1.bsh	Steps through a position list and snaps an image at each position, saving to a multipage TIFF datastore
2DScanning&Camera_implementation_2.bsh	Same workflow using MM2.0's SequenceSettings builder and runAcquisitionWithSettings for tighter integration with the MDA engine
Spectral Mapping.bsh	Full 2D spectral mapping with configurable unidirectional or serpentine scanning, auto-incrementing save paths, and acquisition via the sequence engine

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MM-2.0 — Spectral Mapping (Top-Level)

These two scripts represent the most complete workflows in the repository, intended for spectral mapping experiments where the XY stage scans a sample while a camera images the spectrometer output at each position.

SpectralMapping-1CAM.bsh

Single-camera 2D spectral mapping. The stage performs a grid scan (unidirectional or serpentine), acquiring one spectrum per position. Positions are built into a PositionList and acquisition is handled by runAcquisitionWithSettings. The stage returns to center after acquisition.

SpectralMapping_2CAM.bsh

Dual-camera variant that manually loops through positions and alternately acquires from two cameras (NIRvana HS + Andor) with independent ROI and exposure settings. Each camera's images are accumulated in a separate RAM Datastore and saved independently at the end.

Key advantage: By manually handling each camera sequentially rather than using MM's multi-camera mode, this script can handle cameras with different ROI sizes — something that Micro-Manager's built-in multi-camera support does not allow. The trade-off is that acquisition is slower than hardware-synchronized triggering.

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Notes on Micro-Manager Version Compatibility

The MM1.4 and MM2.0 APIs differ significantly. In particular:

• PositionList / MultiStagePosition imports changed between versions
• The Datastore and Coordinates APIs are MM2.0-only
• SequenceSettings.Builder is MM2.0 only; MM1.4 uses a different acquisition interface

If you are adapting these scripts, make sure your imports match your installed MM version.