In ScanImage 3.0, image data acquired during a GRAB was buffered into (Matlab) memory, and then saved to disk following the acquisition. For applications requiring long imaging records (e.g. optical recording during behavior protocol), this restriction limited the number of frames that could be obtained without either 1) running out of memory or 2) breaking the acquisition into several LOOP iterations, with a 'gap' of time employed to allow for the TIF image data to be written to disk.
To overcome this, ScanImage 3.5 adds the capability to 'stream' to disk continuously. This has been implemented for 'standard mode' operation only. Thus, the new controls can be seen on the Standard Mode Controls window:
New Controls
- Save during acquisition?: When selected, data is streamed to disk continuously during GRAB/LOOP acquisitions. The number of frames that can be entered (# Frames)is unlimited.
- # Frames/File: Some users may prefer to separate ('chunk') data from very long acquisitions into several smaller files. This control specifies the number of frames to log to each file during the acquisition. As further data is collected, a new data file is automatically created. When this option is selected, a three-digit number (e.g. 001, 002, etc) is appended to the filename, following an underscore. The number is auto-incremented as each new file is added. Thus, if 3000 frames are collected with 500 frames/file, with Basename='BehaviorExpt' and Acquisition #=1, specified in the Main Controls window, there will be six files named BehaviorExpt1_001 through BehaviorExpt1_006. If this value is Inf, or the # Frames/File specified exceeds the # Frames, file 'chunking' is disabled, and all data is logged to a single file, named as usual (e.g. BehaviorExpt1).
If acquisition is interrupted, whether by selecting Abort..., or by some other event, data logged to the file has been found, in testing thus far, to be readable and uncorrupted. Thus, file chunking is not generally advised/required.
ScanImage 3.5 writes image data to uncompressed TIF files, as did ScanImage 3.0. Files can become quite large. The use of data compression will be added in future versions.
One variable related to this feature has been added to the standard_model.INI file:
maxBufferedGrabTime: Specifies the maximum duration, in seconds, to allow a GRAB acquisition to proceed with Save during acquisition? option not selected. If long acquisitions are desired without streaming-to-disk, then this number can be increased. The maximum value reached will depend on computer memory. Increasing/adjusted this value is not generally recommended.