STANDARD CONTROLS Panel
The settings on the STANDARD CONTROLS panel pertain to ScanImage capabilities for complex image acquisitions – such as Multi-Frame Acquisitions, Image Stacks, and [*LOOPS*].
Multi-Frame Acquisition Settings
ScanImage allows multiple frames to be acquired continuously, without interruption (i.e. gap-free). The acquisition of multiple frames is initiated by a single trigger.
- Unknown macro: {blue}Specifies the number of frames to be acquired per trigger, which marks the start of a GRAB or LOOP Repeat or the start of each individual Slice in an Image Stack acquisition.
If
Unknown macro: {blue}is disabled, then the acquired data will be stored as a multi-page TIF file consisting of C * Z * N images, where C is the number of Channels stored, Z is the specifiedUnknown macro: {blue}, and N is the specifiedUnknown macro: {blue}
The value Inf (infinity) can be entered for continuous imaging (with data file streaming, if
Unknown macro: {blue}is enabled) untilUnknown macro: {blue}is pressed
- Unknown macro: {blue}Indicates that the specifiedUnknown macro: {blue}should be aveaged, rather than individually stored and/or displayed.
If enabled, the image display for each Channel will show the accumulating average, i.e. improving in signal-to-noise ratio with each Frame
If enabled, the averaged data will be stored to the image file as a single frame. The TIF file may still be a multi-page TIF file, however, e.g. consisting of C * Z images, where C is the number of Channels stored and Z is the specified
Unknown macro: {blue}.
Image Stack Settings
When the value of
is greater than 1, an Image Stack acquisition is implied. Image Stack acquisitions consist of multiple Slices, corresponding to different axial (Z) positions. Each Slice is individually triggered and consists of a Frame or set of frames as specified by
- Unknown macro: {blue}Specifies the number of Slices to collect during the Image Stack acquisition
- Unknown macro: {blue}Specifies the axial (Z) step to take with the stage/motor controller between each Slice
Either a positive or negative value can be specified, so the motion may proceed in either axial direction
- Unknown macro: {blue}: Specifies that stage/motor controller returns to the Home position – the initial position when GRAB or LOOP is pressed – following the GRAB acquisition or LOOP Repeat, so that subsequent acquisitions or Repeats occur at the same axial positions.
If this option is not selected when using LOOP mode, then successive Repeats will image further along the axial direction specified
The first acquisition in the Image Stack (or first Image Stack within a LOOP acquisition) consists of the Home position – i.e. the motor does not move until after the first Slice.
At this time, external triggering is not supported for Image Stack acquisitions
Using Start/End Limits
The
panel provides an option where
. With this option, two axial positions can be identified by the user (i.e. while using FOCUS mode) as the boundaries of the Image Stack to collect. The
and
parameters will then obey the start/end position constraint – i.e. the
is automatically updated by the start/end position values, and each of
and
updates the other value. See MOTOR CONTROLS for further details.
LOOP Mode Settings
- Unknown macro: {blue}When operating in LOOP Mode, this determines the total time following the trigger of each LOOP Repeat to wait before ScanImage generates trigger to begin the next Repeat. In other words, this specifies the trigger-to-trigger time between Repeats.
The specified time should be at least as long as the acquisition during each Repeat plus any post-acquisition processing.
When a Stack Acquisistion is employed, this value indicates the time for the entire stack, and specifically the time between the ScanImage triggers issued for the first slice of each Repeat
This setting only has effect when internal triggering is employed
Unknown macro: {multi-excerpt}- Unknown macro: {blue}Specifies the number of Repeats to be acquired for each LOOP acquisition
Value of Inf (the default) can be entered so that LOOP acquisition will continue indefinitely until
Unknown macro: {blue}is pressed
Continuous TIF Streaming
- Unknown macro: {blue}Enables ScanImage capability for continuous TIF streaming during GRAB or LOOP mode acquisitions. This causes data to be stored to the image file as each Frame arrives during an acquisition, as opposed to the default ScanImage behavior of buffering acquired data and saving to disk at the completion of the acquisition.
Selecting this option avoids out-of-memory errors associated with acquisitions consisting of large
Unknown macro: {blue}and/orUnknown macro: {blue}values
Selecting this option reduces the processing time following acquisitions, allowing for LOOP _Repeats to occur with a smaller
Unknown macro: {blue}, or smaller gap between when an external trigger can be processed.
At this time, the
Unknown macro: {blue}option is not supported for:- Image Stack acquisitions
- acquisitions involving the Power Box feature.
- acquisitions where
Unknown macro: {blue}is enabled
- Unknown macro: {blue}Some users may prefer to separate ('chunk') data from very long acquisitions into several smaller files. This value 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.
To disable such 'chunking', this value should be set to 'inf' (infinity), causing all data to be logged to a single file.
When chunking is enabled, 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 ('chunk') is added. For example, if 3000 frames are collected with 500 frames/file, with
Unknown macro: {blue}='BehaviorExpt' andUnknown macro: {blue}=1, specified in theUnknown macro: {report-info}panel, there will be six files named 'BehaviorExpt1_001' through 'BehaviorExpt1_006.
Pseudo-Focus Mode
If
is set to 0, then no data will be stored, nor buffered, during a GRAB or LOOP acquisition. This is termed 'pseudo-FOCUS' mode. The mode is useful for FOCUS like applications where the user requires 1) external triggering, 2) control over the
, and/or 3) execution of a [_User Function_] during each Frame.