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General

  • About
    • Downloading ScanImage®
      • Citing ScanImage®
      • Software Level
      • Free ScanImage®?
    • Publications
    • Support
    • ScanImage® Changes
      • 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
        • 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
    • User and Configuration Settings
      • Loading & Saving CFG & USR Files
      • User Settings (USR) 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
      • 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 Terminals

Tutorials

  • Configuration Tutorial
  • Basic Features
    • Acquisitions
      • Focus
      • Grab
      • Loop
    • Beam Management
      • Calibration
      • Changing Beam Power
      • Automatic Depth Power Adjustment
      • Specifying Beam Power for rectangular ranges within a Scanfield
      • Other Beams Usage
    • Stage and Fast Focus Controls
      • FastZ Alignment
        • Prerequisites
        • Procedure
    • Stack Acquisition
      • Slice Configuration
      • Stack Type
        • Slow Stack
        • Fast Stack
      • Starting the Acquisition
      • Render as Volume
        • Current Limitations
    • Alignment between Stage and Scanner
      • Manual Shift method
      • 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
    • WaveSurfer Yoking
    • Pixel Multiplication with the vDAQ
      • Setup
      • Resonant Profile Constant Coefficient Multiplication Examples
    • Generating a ScanImage® Report for Issue Submission
  • Premium Feature Tutorials
    • Alignment
      • Tutorial
      • Camera 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
      • API
    • Arbitrary Line Scanning
      • Hardware Requirements
      • Using Arbitrary Line Scanning in ScanImage
        • Scan Path Design
        • Using the Stimulus Editor
        • Executing a Line Scan
      • Verifying the Scan Path
        • Reading Line Scanning Data Files
      • Analysis
    • Photostimulation
      • ScanImage® Photostimulation Requirements
      • Configuration
      • 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
    • Photon Counting
      • Photon Counting with High Speed vDAQ
        • Hardware Setup
        • Software Tutorial
      • Photon Counting with NI High Speed Digitizer
        • Hardware requirements
        • Configuration
        • Principle of Operation
    • 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
    • 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
  • Advanced Features
    • ScanImage® API
      • RoiGroup and Roi API
        • Roi Hierarchy
        • RoiGroup
        • Roi
      • RotatedRectangle API
        • Rotated Rectangle Imaging Scanfield
        • Pixel Positions in Reference Space
        • RoiManager
      • Stimulus Field
        • Stimulus Scanfield
        • Stimulus Sequence
      • IntegrationField API
        • Integration Scanfield
    • User Functions
      • Controls
      • User Function Definition
        • A Very Very Brief Example
      • Events
        • General Events
        • Photostimulation-module Events
    • Custom Stimulus Functions
      • Example

Appendix

  • Safety
  • Glossary
  • Windows Reference Guide
    • Startup Configuration
      • Overview
    • Alignment Controls
      • Overview
      • Main Panel
      • Reference Image Panel
    • Cameras
      • Configuring a Camera
      • Accessing Configured Cameras
      • Camera Controls Interface
      • Camera to Scanner Alignment
    • Channel Display Window
      • Live Histogram
    • Channels
      • Per-Channel Controls
        • Merge Display Controls
        • Other Channel Controls
    • Configuration Controls
      • Imaging System
      • Acquisition Parameters
      • Advanced Timing Controls Panel
      • Line Scan Controls
    • Cycle Controls
      • Cycle Mode Overview
      • Left Side Controls
      • Right Side Controls
        • Cycle Iteration Data Table Edit Tools
        • Cycle (CYC) File Format
    • Data Scope
    • Fast Configuration
      • Description
      • Controls
      • Notes
        • Activating Fast Configuration
        • Keyboard hotkeys
    • Stack Controls
      • FastZ Tuning Window
        • Introduction
        • Actuator Tuning Window Controls
        • Examples
      • Stack geometry definition
      • Stack mode
      • Slow Stack
      • Fast Stack
      • Uniform
      • Bounded
      • Arbitrary
    • Image Controls
      • White/Black Levels
      • Frame Averaging and Volume Display
      • Channel Display Buttons
    • Laser Trigger Scope
      • Overview
      • Main Panel
    • Line Scanning Channel Display Window
      • Introduction
      • Full Data View
      • Time Plot
      • Spatial View
    • Main Controls
      • User Settings / Config
      • Acquisition Parameters
      • Logging Controls
      • Acquisition Start Controls
      • ScanField Parameters
      • MROI & PhotoStim Launch
      • Fast Configuration Buttons
      • MAIN CONTROLS Panel - File Menu
      • MAIN CONTROLS Panel - Settings Menu
      • MAIN CONTROLS Panel - View Menu
    • Motion Display Window
    • Motor Controls
      • Motor Alignment Window
      • Overview
    • Photon Counting Controls
    • Photostimulation Controls
      • Overview
      • Main Panel
      • Sequence Mode
      • On-Demand Mode
      • Stimulation Controls
    • Power Controls
      • Power Box Controls
        • Overview
        • Main Panel
        • Selected Power Box Settings Panel
      • Overview
      • Main Panel
      • Selected Beam Panel
    • ROI Integration Windows
      • Integration Control Window
      • ROI Integrator Traces Window
    • ROI/Stimulus Group Editor
      • Custom Cell Pick Segmentation Routines
        • Writing Custom Cell Pick Functions
      • Overview
      • ROI Display
      • ROI Group Table/ROI Group Controls
      • New ROI Panel
      • Selected ROI/Scanfield Properties Panel
      • Stimulation Quick Add Panel
      • Using the Cell Picker
      • Hotkeys
    • Scanfield Display Controls
      • Introduction
      • Scanfield Display Table
      • Display Settings
    • Signal Conditioning Controls
    • SLM controls
    • Status Window
    • Trigger Controls
      • Description
      • External Trigger Configuration
      • External Trigger Test Panel
    • User Functions
      • Description
      • Controls
      • Code
      • A Very Very Brief Example
      • Events
        • General Events
        • Photostimulation-module Events
    • User Settings
      • Description
      • Controls
        • Buttons
        • Current USR Properties Table
        • User Property Set Table
      • Command Window
    • Waveform Controls
      • Waveform Controls
      • Waveform Display Controls
  • 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
    • Failed to read scanner frequency
    • PMT Ripple Noise
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