Space Details:

Key	SI2016
Name	ScanImage 2016
Description
Created by	ed@vidriotech.com (Feb 16, 2015)

Available Pages:

ScanImage 2016
- ScanImage Home
- Getting Started Guide
  - Setting Up ScanImage
    - Manually Installing ScanImage
  - Software Version Compatibility
  - Supported Microscope Hardware
    - Acquisition and Control Hardware
    - ScanImage core scanner support
  - Wiring Guide
    - Configuring ResScan (Resonant Scanning)
    - Configuring LinScan (Galvo Galvo scanning)
    - Thorlabs Scope Wiring
    - Synchronizing ResScan and LinScan
    - Shutter Configuration
    - Wiring ScanImage analog input terminals
    - Configuring SlmScan (SLM Scanning)
  - Motor (Stage Controller) Setup
  - ScanImage Upgrades
    - ScanImage 3.8 to SI5.1 Upgrade
    - ScanImage 4 to SI5.1 Upgrade
    - ScanImage 3.x upgrade guide
- Window Reference Guide
  - Startup Configuration
  - Alignment Controls
  - Channel Display Window
    - Live Histogram
  - Channels
  - Configuration Controls
  - Cycle Controls
  - Fast Configuration
  - Fast Z Controls
    - FastZ Tuning Window
  - Image Controls
  - Line Scanning Channel Display Window
  - Machine Configuration Editor
    - Analog Stage Controller Settings
    - Closed-Loop Experiment Outputs Settings
    - FastZ Actuator Settings
    - General ScanImage Settings
    - Linear Scanner Settings
    - Photostimulation Settings
    - PMT Controllers Settings
    - Power Modulation (Beams) Settings
    - Resonant Scanner Settings
    - Shutter Configuration Settings
    - Stage Controllers (Motors) Settings
    - ThorLabs BScope2 Settings
    - ThorLabs ECU Scanner Settings
  - Main Controls
  - Motion Correction Windows
  - Motor Controls
    - Motor Alignment Window
  - Photostimulation Controls
  - Power Controls
    - Power Box Controls
  - PMT Controls
  - ROI Integration Windows
  - ROI/Stimulus Group Editor
    - Custom Cell Pick Segmentation Routines
  - Scanfield Display Controls
  - Status Window
  - Trigger Controls
  - User Functions
  - User Settings
  - Waveform Controls
  - SLM controls
- Concepts Guide
  - Arbitrary Line Scanning
    - Configuring the Arbitrary Scan Path
    - Reading Line Scanning Data Files
  - Pockels Cell Concepts
  - Beams
  - CFG and USR Files
  - Configuring Photon Counting Modules
  - Fast Z
    - Using the Actuator Tuning Window
  - Linear Scanning Concepts
    - Striping Display
  - Machine Configuration Editor Concepts
  - Machine Data File
  - Motion Correction
  - Motor (Stage) Alignment
  - Multiple Region of Interest (MROI) Imaging
    - ROI API
      - RoiGroup & Roi API
      - Scanfields API
        
        IntegrationField API
        
        RotatedRectangle API
        
        StimulusField API
      - IntegrationROI PostProcessing
    - Scanfields, ROIs, ROI Groups
    - ScanImage Coordinate Systems
    - Scanner Configurations
  - Photostimulation
    - Creating Stimulus Groups
      - Built-in and Custom Stimulus Functions
    - Triggering Stimulus Patterns
      - On-Demand Mode
      - Sequence Mode
    - SLM Photostimulation
    - Scanner Alignment
    - Monitoring and Logging
    - Photostim Motion Correction
  - PMT Signal Offset Correction
  - Resonant Scanning Concepts
    - Calibration of the resonant scanner's amplitude at different zoom levels
    - Fill Fraction
    - Line Formation
    - Period Trigger
    - Scan Phase
      - Automatic Scan Phase Compensation for Resonant Scanner Frequency Drift (In Progress)
    - Synchronization to Laser Clock
  - ROI Integration (Online Analysis)
    - Roi Integration Output Channels
  - Scan Control DAQ
  - ScanImage API
  - ScanImage Safety
  - Scanner Alignment Concepts
  - SI 3 Concepts Copy
    - Beam Flyback Blanking
    - Fast (X) Scan Optimization
    - Physical Scanner Limitations
    - Slow (Y) Scan Dimension Basics
  - Slow Stacks
  - Triggering & Synchronization
    - Acquisition Triggering
    - Auxiliary Trigger
    - I2C data recording
  - Command Waveform Optimization
- README
  - ScanImage January 2016 Release Thorlabs BScope 2 Compatibility Information
- How-to articles
- Solutions Guide
  - Aspect Ratio Solutions
    - Optimization of Scanned Images Aspect Ratio
  - Fast Z Solutions
    - Discard Flyback Frames Option
    - Planes Shift Depth during Volume Scanning
    - Step and Settle Mode
    - Varied Z Stack Frame Size
    - Z Actuator Calibration in Microns
  - Flyback Solutions
    - Flyback Resonant Scanning
    - Flyback Signal Output and Start of Acquisition
    - Flyback Time Delay Measurement
    - Frame Rate Drops in Scan Phase Adjustment
    - How Resonant Scanning Flyback Works
    - Unexpected Pauses with the Y-Galvo
  - General Solutions
    - How to Run a ScanImage Simulation
    - ScanImage BigTiff Specification
  - Image Data/Frame Solutions
    - Acquisition Stops Unexpectedly-Frame Data Corrupted
    - Current Scan Status Using API
    - Dynamic Range of Digitizer Raw Data > max(int16)?
    - Error occurs when changing frame size on galvo/galvo
    - Fix rolling frame average calculation
    - Image Value Limits
    - NI 573X Digitizer Module: Over-voltage Protection
  - Linear Scanning Solutions
    - Galvo-Galvo Image Appears Chopped Up
    - How to implement your own LinearStageController
  - Metadata Solutions
    - How Data and Metadata is Stored
    - Where Can a Detailed Metadata Specification be Found
  - Noise Reduction Solutions
    - PMT Causes Diagonal Patterns
  - Photostimulation Solutions
    - Photostimulation Breakout Box and Sample Code
    - Photostimulation Capability SI Versions and Demos
    - Photostimulation Timing Mechanism
  - PMT Solutions
    - Diagonal Patterns Appear when PMTs On and Laser Off
  - Regions of Interest (ROI) Solutions
    - scanimage.si.hRoiManager.linPeriod
  - Resonant Scanning Solutions
    - Not Getting Square Images as Zoom In
  - ScanImage Hardware Questions
    - Analog Input Speed for NI PXle-6341 Device
    - Bundled Hardware Solutions
    - Configuration of Uniblitz VMM-D1 Shutter Controller
    - Coupling Serial Device to Acquisition
    - Daq Card Sharing
    - Issue getting NI Flex Rio Chassis to work
    - Scanning Hardware
    - Shutter Support
    - Supported Scientifica Stage Types
  - ScanImage Licensing/Support Questions
    - ScanImage 5.x Copyright License
    - ScanImage Support
  - ScanImage Premium Features
  - ScanImage Report Solutions
    - Generating a ScanImage Report for Issue Submission
  - ScanImage Upgrade Questions
    - Upgrade ScanImage 3.8 to ScanImage 5.2
    - Upgrade ScanImage 4 to SI5
  - Shutter Solutions
    - How to Trigger the Shutter Separately from Stop Acquisition
  - Wavesurfer Integration
    - Controlling ScanImage from WaveSurfer
    - Set Up of ScanImage-Wavesurfer Intercommunication
  - Window Controls Solutions
    - Power Control Only Works with "Direct Mode" Checked
- ScanImage Utilities
  - Computer Resonant Scan Mask
  - Daq Task Get Max Sample Rate
  - Generate Multi-ROI Data From Tiff
  - Generate ROI Data From Image
  - Generate ScanImage Report
  - Open Tiff
  - Pulse Generator
  - Read Photostim Monitor File
  - Read ROI Group From Appended Tiff Data
  - Reset Class Data Files
  - Reset Daq Devices
  - Reset Mirror Sim
  - Translate Trigger To Port
- Tutorials
  - ScanImage API: Creating a simple user interface
  - Match current field of view with previous session
- Glossary
- Archive
  - Error Messages and Solutions
  - ScanImage 5 Info
  - Imaging Guide
  - How to Set Up Your ScanImage Development Environment
  - Cell Picker Controls
  - Copy of Power Controls
- internal documentation
  - LinScan specs
    - Device Utilization
    - Galvo Device Synchronization
    - Live AO update
    - Tiff write performance
    - Triggering + Timestamping
  - Setup Visual Studio to work with NIFPGAMEX
  - Howto Embed a Youtube video
Making a template