Introduction
ScanImage controls a laser scanning microscope such as a 2-photon or confocal. It is written entirely in Matlab 6.1 and makes use of standard National Instruments boards for data acquisition and scanning output. The software generates the voltage used to drive the scan mirrors, acquires the raw data from the photomultiplier tubes, and processes these signals to produce sub-micron resolution images. Up to three channels (12-bits each) can be acquired simultaneously, and the software is written to be easily expandable to the maximum number of channels the NIDAQ board supports. The software runs at nearly real-time rates even when acquiring on three channels simultaneously, updating the images with minimal delay from the time they are actually obtained. Virtually no specialized hardware is required for either scan mirror motion or data acquisition.
Features
- Realtime Focusing on Multiple Channels
- Programmable Configurations and Windows Setups
- Instant Image Zooming, Rotation, and Offsetting
- Collection Modes include:
- Frame Scans
- Line Scans
- Kalman Filtering
- 3D or 4D Stacks
Installation
- Download the ScanImage_Installation.zip file from the Svoboda Lab Software page and save it to your computer.
- Extract to the MatlabRoot\work directory, making sure that pathnames are preserved in the extraction by selecting the checkbox in the extraction utility.
- Press the Unzip button.
- Start Matlab and execute the following command (cut and paste into Matlab command window): >> addpath(genpath(fullfile(matlabroot, 'work','ScanImage_v2.0_r1.0')));
>> path2rc - Installation is complete. Exit Matlab and when you restart Matlab, an icon will appear allowing you to select ScanImage. See the documentation for details (contained in the folder: MatlabRoot\work\ScanImage_v2.0_r1.0\documentation)