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
3D Shot Holographic Targeting
Previous
Next
3D Shot Holographic Targeting
TO DO