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General

  • About
    • Downloading ScanImage®
      • Citing ScanImage®
      • Software Level
      • Free ScanImage®?
    • Publications
    • Support
    • ScanImage® Changes
      • 2026.0.0
        • New Universal Features
        • Device Support
        • New Premium Features
        • General Improvements
        • Compatibility
      • 2023.1.0
        • New Universal Features
        • New Premium Features
        • Device Support
        • GUI Tweaks
        • Bug fixes
      • 2023.0.0
        • New Universal Features
        • New Premium Features
        • Device Support
        • GUI Tweaks
        • Bug Fixes
      • 2022.1.0
      • 2022.0.1
      • 2022.0.0
      • 2021.1.0
      • 2021.0.0
      • 2020.1.4
      • 2020.1.3
      • 2020.1.2
      • 2020.1.1
      • 2020.1.0
      • 2020.0.0
      • 2019bR1
      • 2019bR0
      • 2019aR1
      • 2019aR0
      • 2018bR1
      • 2018b
      • 2018a
      • 2017b
      • 2016b
  • Configuration
    • PC Configuration
      • PC Requirements
      • Install Matlab
      • DAQ Installation
        • vDAQ Installation
        • NI DAQ and driver Installation
      • Install ScanImage
      • Run ScanImage
    • Licensing
      • License Management (SI2022+)
        • Online Activation
        • Offline Activation
      • Legacy License Manager (SI2020-SI2021)
        • License File
      • Data Collection
    • Machine Data File
    • Devices
      • DAQ
        • vDAQ Configuration
        • Resonant Scanning NI DAQ Configuration
        • Linear Scanning NI DAQ Configuration
      • Scanners
        • Analog Galvo
        • Resonant Scanner
        • Generic Polygonal Scanner
        • Vidrio RMR
        • Mirrorcle Resonant Scanner
        • Thorlabs ECU 1 - Scanners
        • Thorlabs ECU 2 - Scanners
      • PhotoMultiplier Tube
        • Analog PMT Controller
        • Thorlabs PMT2000/2100
        • Thorlabs PMT2100 v2
        • Thorlabs ECU1 - PMT
        • Thorlabs ECU 2 - PMT
      • Beam Modulators
        • Fast Beam Modulator
        • Beam Router
        • Motorized Half-Wave Plate
        • Thorlabs BCM-PA
      • Motor Controller
        • Zaber Stages
        • Thorlabs MCM 3000
        • Thorlabs MCM 6000
        • Thorlabs Kinesis Controllers
        • Analog Motor Controller
        • Legacy Motor
        • Scientifica Motion 8
        • Sutter MPC200
        • Sutter MP285A
        • Sutter MP285
        • PI Motor Controllers
        • Sensapex uM
      • Fast Focus
        • Analog FastZ
        • PI GCS1
        • PI GCS2
        • LC40x FastZ
        • Thorlabs PFM450
        • Thorlabs Liquid Crystal Analog FastZ
      • Shutter
        • Digital Shutter
      • Camera
        • FLIR Spinnaker Camera
        • DCAM Configuration
        • MicroManager Camera
        • Simulated Camera
      • Spatial Light Modulators
        • Generic Monitor SLM
        • Meadowlark SLM 1920x1152
        • Meadowlark SLM ODP 512x512
        • Simulated SLM
        • Thorlabs Exulus SLM
      • Picoquant Remote Interface
        • Setup
        • FAQ
      • Miscellaneous Devices
    • SI Coordinate Systems
      • Configuration
      • Files
    • SI Motors
      • Basic tab
      • Advanced tab
    • Imaging Systems
      • vDAQ Scan System
      • NI Resonant Scan System
      • NI Linear Scan System
      • SLM Scan System
    • Layout and Configuration Settings
      • Loading & Saving Layout & CFG Files
      • Layout Files
      • Configuration (CFG) Files
  • Concepts
    • Scanner Configurations
      • Linear Scanning
        • Performance
        • Compatible Premium Features
        • Striping Display
      • Resonant Scanning
        • Fill Fraction
        • Line Formation
        • Period Trigger
        • Scan Phase
    • ScanImage® Coordinate Systems
      • Scanner Coordinates
      • Reference Coordinates
      • Sample Relative Coordinate System
      • Scanfields, ROIs, ROI Groups
        • Scanfields
        • ROIs
        • ROI Group
    • Sample Coordinate System
      • Motor Controls
      • Sample Coordinates: Lateral
      • Sample Coordinates: Axial
      • API
    • Volume Imaging
      • Slow Volumes/Stacks
      • Fast Volumes/Stacks
      • Waveform and Buffer
        • Waveform Types
    • Beams
      • Control and Timing
      • GUI
      • Calibration
        • Data Collection
        • Data Processing
        • More considerations
    • Triggers
      • Acquisition Triggering
        • Acquisition Start Trigger
        • Next File Marker
        • Acquisition Stop Trigger
      • Auxiliary Trigger
        • Auxiliary Trigger Wiring
        • Debouncing
      • I2C data recording
        • Wiring
        • Software
        • I2C packet format
        • Data format
        • Emulate I2C master using a NI-DAQ board
      • Exported Clocks
        • Clock Definitions
        • Clock Terminals

Tutorials

  • Configuration Tutorial
  • Basic Features
    • Acquisitions
      • Focus
      • Loggable Acquisitions
      • Grab
        • Logging Parameters
      • Loop
    • Beam Management
      • Calibration
      • Changing Beam Power
      • Automatic Depth Power Adjustment
      • Scanfield Power Boxes
      • Other Beams Usage
    • Stage and Fast Focus Controls
      • Stage Controls
      • Fast Focus Controls
    • FastZ Alignment
      • Prerequisites
      • Procedure
    • Stack Acquisition
      • Slice Configuration
      • Stack Type
        • Slow Stack
        • Fast Stack
      • Starting the Acquisition
      • Viewing Images
        • Pinning Images
        • Power Over Depth
    • Alignment between Stage and Scanner
      • Motion Correction method
        • Automated calibration
      • Symbols
      • API
    • Motion Estimation and Correction
      • Setup
      • Motion Estimators
      • Motion Correctors
      • Match Current FOV with Previous Session
      • Output Files
      • API
        • Motion Estimators
        • Motion Correctors
      • Using Averaged frames
    • Configuring Photon Counting Modules
      • Hardware Configuration
      • ScanImage® Configuration
      • Limitations
    • Synchronization to Laser Clock
      • Hardware Configuration
      • Using the AD-951X Evaluation Board
      • ScanImage® Configuration
        • Configuration with the vDAQ
        • Configuration with NI DAQs
      • Troubleshooting
        • Laser Clock Signal Quality
        • Sampling Phase Delay
        • Anti-Aliasing Filter
    • Data Scope Concepts
      • Noise Sources
    • Offline Data Viewer
      • Using the Offline Data Viewer
        • Time Slider
        • Image View
        • Plot View
      • Rendering Frame Sequences
    • vDAQ Analog Data Recorder
      • Data Recorder Configuration Page
      • Controlling the Data Recorder
      • Data Recorder HDF5 Files
    • Waveform Generator
      • Device Compatibility
      • Hardware Config
      • Software Config
        • Definitions
      • Defining Custom Waveforms
        • Waveform Parameters
      • Waveform Optimization
    • Externally Triggerable Scripts
      • Device Compatibility
      • Hardware Config
      • Software Config
        • Definitions
      • Widget
    • Pixel Multiplication with the vDAQ
      • Setup
      • Resonant Profile Constant Coefficient Multiplication Examples
    • Generating a ScanImage® Report for Issue Submission
  • Premium Feature Tutorials
    • Scanner to Scanner Alignment
      • Motivation
      • Tutorial
        • Camera Alignment
    • Session-Session Alignment
    • Multiple Region of Interest (MROI) Imaging
      • Benefits
        • Frame Rate Optimization
        • Limiting Tissue Exposure
        • Tracing of features through a volume
      • Using MROI
      • Output File
    • Waveform Optimization
      • Wiring
        • Cambridge Galvo mirrors
        • Fast-Z
      • Operation
      • Advanced
        • Number of Signals
        • Moving Window Size
      • API
    • Arbitrary Line Scanning
      • Use Cases
      • Prerequisites and hardware requirements
      • Step by Step Guide
        • Add Reference Image
        • Add ROIs
        • Draw in the viewport
        • Select function and its parameters
        • Editing the scan path
        • Executing a Line Scan
      • Verifying the Scan Path
      • Reading Line Scanning Data Files
        • Using the ScanImage® Utility
        • Manually Decoding Data Files
      • Analysis
    • Photostimulation
      • Photostimulation Requirements and Capabilities
        • Hardware Requirements
      • Configuration
        • Logging
        • Output TTLs
      • Create Stimulus Groups
        • Built-in Stimulus Functions
      • Triggering Stimulus Groups
        • Sequence Mode
        • On-Demand Mode
      • Photostim Motion Correction
        • Galvo Controller Board Configuration
        • Wiring
        • MDF Configuration
        • Operation
      • SLM Photostimulation
        • Setup
        • Registration
        • Zero order diffraction
      • Output Files
    • ROI Integration (Online Analysis)
      • Integration ROIs
      • Calculation of Intensity
      • Output File Format
      • Programmatic ROI access
      • ROI PostProcessing
        • Default function
        • Example: Average last three values
        • Performance optimization
        • Application example
      • Motion Correction
      • Output Channels
    • ROI Integration Output Channels
      • Channel Configuration
      • Output Configuration
      • User-defined output function
    • Temporal Demultiplexing
      • Prerequisite
      • Tutorial
    • Light Beads
      • Configuration
      • Use
      • Alignment
      • Output File
    • Photon Counting
      • Hardware Setup
        • Time Correlated Photon Counting
      • Software Tutorial
        • Photon Counting
        • Virtual Channels
        • Time Correlated Photon Counting
    • SLM Photostim Calibration and Alignment
      • Phase LUT Calibration
      • SLM Flatness Correction
      • Align Linear Scanner to Imaging
      • Laterally Align the SLM
      • Align SLM Z to stage Z
      • Laterally Align the SLM through Z
    • Acquisition Gating for low rep rate Lasers
      • On the vDAQ
        • Standard vDAQ
        • High Speed vDAQ
      • On National Instruments hardware
    • ScanImage® Remote Control (TCP/IP)
      • Matlab Remote Server
      • Matlab Remote Client
      • ScanImage® Control
    • 3D Shot Holographic Targeting
    • SLM Diffraction Efficiency Calibration
      • Calibration Steps
    • Tile Manager
      • Components
        • Tile View
        • Tile Objects
        • Tile Scanning
        • Tile Sorting Functions
        • Scan Tile Tools
        • Tile Generators
    • Sample Tracking Power Boxes
      • Prerequisites
        • Hardware
        • Alignments
      • Tutorial
        • Aquiring a preview image
        • Adding a Power Box
        • Overlaying the power box over the context image
        • Power Box Power
        • About Power Box Mask
        • Setting Power Box mask from a context image
        • Painting the mask
        • Executing the power box
      • Caveats
    • vDAQ Multiple Imaging Arm Acquisition
      • Configuration Procedure
      • Startup Procedure
      • Helpful Tips
      • Example Window Configurations
    • Stage Scanning
      • Configuration
        • Mechanical Considerations
        • Electrical Considerations
        • Software Considerations
      • Use
        • Performance
        • Combination with other features
        • Planning where to scan
    • FOV Curvature Correction
      • Configuration
      • GUI
        • Axes
        • Settings Panel
        • Sliders
      • Use
      • Tutorial
        • Script
      • Caveats
    • ZeroMQ
      • Protocol Overview
      • ScanImage® Configuration
        • Via Configuration Device
        • Via Command Window
      • Client Information
        • Message Format
        • Example
  • Advanced Features
    • ScanImage® API
      • Introduction
        • ScanImage Scripting API
        • vDAQ® API
        • RoiGroup and Roi API
        • RotatedRectangle API
        • Stimulus Field
        • IntegrationField API
    • User Functions
      • Controls
      • User Function Definition
        • Example
      • Events
        • General Events
        • Photostimulation-module Events
    • Custom Stimulus Functions
      • Example

Appendix

  • Safety
  • Glossary
  • Tab Reference Guide
    • Graphical User Interface
      • Features GUI
    • Viewport
      • Basic Controls
      • Basic Elements in XY
        • Scanner FOV
        • Park Position
        • Default Imaging Group ROI
        • Annotations
        • Motor Controls
        • Scalebar
      • Basic Elements in Z
        • Display Slider
        • Actuator Slider
        • Paired FastZ Dropdown
        • Z Range
        • Stack
        • Motor Controls
        • Stage Drag Limits
        • Absolute Stage Limit
      • Groupings of Elements
    • Alignment Tab
      • Keyboard Shortcuts
      • Resonant Scanner Calibration Panel
      • X Offset Scaling Calibration Panel
      • Stage Scanner Alignment Panel
      • FastZ Alignment Panel
      • Precise FastZ Alignment Panel
      • Scanner To Scanner Alignment
      • Session-Session Alignment Panel
    • Arbitrary Line Scanning Tab
      • Keyboard Shortcuts
      • Arbitrary Line Scan Settings Panel
      • Arbitrary Line Scan Rois Panel
      • Arbitrary Line Scan Scanfields Panel
      • Line Scan Display Panel
        • Arbitrary Line Display Style
    • Camera Tab
      • Keyboard Shortcuts
      • Camera Controls Panel
      • Camera Histogram
        • Histogram Controls
      • Camera Alignment
    • Cycle Tab
      • Cycle
      • Time-Lapse
    • Display Tab
      • Scan Phase Controls
      • Histograms
      • Layers
      • Channels
      • Background
        • Image Controls
        • Grid Controls
        • Annotation Controls
    • Edit Stim Groups Tab
      • Stim Scanfields Panel
        • Stimulation Parameters
        • ROI Positioning
        • Optional Parameter
        • Beam Modulator
      • Stim ROIs Panel
    • Field Curvature Tab
      • Example Video
      • Surface Parameters Gui
    • IO Tab
      • Acquisition Triggering GUI
      • User Functions
    • Mosaic Tab
      • Keyboard Shortcuts
      • Mosaic Panel
      • Add Mosaic Panel
    • Motion Tab
      • Motion Estimator Panel
      • Motion Corrector Panel
    • Multiple Regions Of Interest Tab
      • Keyboard Shortcuts
      • Scanfields Panel
      • Rois Panel
        • Buttons
        • Table
        • Add ROI settings buttons
      • Roi Groups Panel
    • Online Analysis Tab
      • Keyboard Shortcuts
      • Integration Scanfields Panel
      • Integration ROIs Panel
      • Integration Output
    • Photostim Tab
      • ROI Groups Panel
      • Settings Panel
        • Scanner and Triggers
        • Monitoring
      • On Demand Settings
        • External Stimulus Selection
      • Sequence Mode Settings
    • Power Box Tab
      • Keyboard Shortcuts
      • Power Boxes Gui
        • Buttons
        • Power Box Table
      • Selected Power Box Gui
        • Basic Settings
        • Mask
    • Quick Analysis Tab
      • Keyboard Shortcuts
      • Quick Analysis ROIs
      • Quick Analysis Scanfields
    • Scan Tab
      • Panel Utility Buttons
      • Scanner Configuration Panel
      • Single Scanfield Settings Panel
      • XY Panel
        • Transitions
        • Sampling
        • Line phase
        • Images
      • Beams Panel
    • Stack Tab
      • Example Video
      • Keyboard Shortcuts
        • Bounded Stacks
        • Arbitrary Stacks
      • Stack Definition Panel
        • Top Panel
      • Stack Actuation Panel
        • Slow Tab
        • Fast Tab
      • Power over Depth Panel
  • Output Files
    • ScanImage® BigTiff Specification
      • Tiff Header Section
      • ScanImage® Static Metadata Section
        • Magic Number
        • ScanImage® Tiff Version Number
        • Non-Varying Frame Data Length
        • ROI Group Data Length
        • Non-Varying Frame Data
        • ROI Group Data
      • Frame Section
        • IFD Header Section
        • IFD Tags
        • Next IFD Location
      • Image Section
  • ScanImage® Utility Functions
    • Compute Resonant Scan Mask
    • Daq Task Get Max Sample Rate
    • Generate Multi-ROI Data From Tiff
    • Generate ROI Data From Image
    • Generate a ScanImage® Report
    • Open Tiff
    • Pulse Generator
    • Read Photostim Monitor File
    • Read ROI Group From Appended Tiff Data
    • Reset Class Data Files
    • Reset DAQ Devices
    • Simulate a Resonant Mirror
    • Translate Trigger To Port
    • Calculate AD951X configuration parameters
  • ScanImage® TiffReader

Solutions

  • Solutions
    • FAQ
      • Failed to read scanner frequency
      • PMT Ripple Noise
    • Patches
      • Standard vDAQ MSADC initialization failure
        • Versions Affected
        • Patch Instructions
ScanImage
  • Premium Feature Tutorials
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Premium Feature Tutorials

These features are available after purchase of a premium license. Click the links below to learn how to use them.

  • Alignment

    • Perspective Alignment Between Multiple Scanners

    • Alignment Between Stage and Scanner

    • Camera Support for Widefield Alignment

    • Session Session-Alignment

    • SLM Photostim Alignment

  • Multiple Regions of Interest (MROI) Imaging

  • Sample Tracking Power Boxes

  • Waveform Optimization

  • Arbitrary Line Scanning

  • Photostimulation

  • SLM Calibration and Alignment

  • Online analysis (ROI Integration)

  • Closed Loop Experimentation

  • Temporal Demultiplexing

  • Light Beads Microscopy

  • Photon Counting with high speed digitizer

  • 3-Photon Imaging Acquisition Gating for low rep rate Lasers

  • ScanImage® Remote Control

  • Multiple Independent Imaging Arm Acquisition with the vDAQ

  • Stage Scanning

  • Curvature Correction

  • ZeroMQ

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