Configuration (r4.1)

CONFIGURATION Panel

: Displays name of currently loaded Configuration (CFG) file. If none loaded, field is blank.

/: Launch dialogs to load CFG file or save current Configuration to specified CFG file.

: Save current Configuration to named (CFG) file.

: Number of pixels per horizontal line to capture in each acquired image (frame). Must be one of the selectable power-of-2 values.

: Number of horizontal lines to capture in each acquired image (frame). Currently, in ScanImage 4.1, value must also be a power-of-2.

Pix=Line: If selected, the values of and are constrained to be equal, e.g 512x512, 256x256, etc.
If constraint is enabled, need only select from menu options to specify pixelation.

: If selected, the value of on the MAIN CONTROLS is constrained to match the fraction ()/(). This constraint implies that dimensions of each pixel are square. Without this constraint, individual pixels may have rectangular aspect ratio.

: (Read-only) Estimated time, in us, for each scanned line. Estimated from specified scanner frequency in Machine Data File.

: If enabled, Bidirectional Imaging is used, i.e. image pixels are collected on both directions of each period's sinusoidal scan trajectory.

: Displays last-measured frame rate at currently set values of , , and (MAIN CONTROLS). If no measurement has ever been taken at this triad of current parameters, value will show NaN in red.
Frame rate MUST be measured at current parameters before start of a GRAB/LOOP acquisition
Measured value at each triad of parameters is stored across ScanImage sessions, i.e. so value need not typically be measured again. In testing thus far, scan rate stability at given settings has been quite stable.

: Measure scan frame rate (average period between Frame Clock pulse edges) at current triad of , , and values.

: (Read-only) At high frame rates (i.e. at low values of ), it becomes required to divide the display rate by an integer decimation factor (displayed here), to reduce load on CPU and ensure critical operations such as disk logging all frames occur without data loss.

The controls are used to adjust which portion of each line scan period is used for imaging, i.e. to center the specified on the scan trajectory for each half scan period.

For Bidirectional Imaging, setting the optimal value ensures that every-other-line in the image is aligned.
For Unidirectional Imaging ( off), the same optimal value ensures that pixels are uniformly spaced, i.e there is no image stretching (occurs when imaging is off-centered with respect to scan sinusoid).

ScanImage 4.1 supports two types of adjustment - hardware and software.

Hardware Scan Phase corresponds to adjustment of digital potentiometer within Thorlabs ECU, directly adjusting phase of line clock edge for each scan period.
Digital potentiometer is available in current Thor ECU builds.
Value specified in arbitrary units from 0-254.
Optimal hardware scan phase will vary for each value

Software Scan Phase adjusts which acquired data samples within each scan period are used for image pixels, i.e. relative to the line clock edge.
Value specified in arbitrary units from -128 to 127.
Optimal software scan phase (at given hardware scan phase) will vary for each set of the following three parameters: , , and # acquiring channels (save and/or display) specified in CHANNELS window

Users are directed to maximize use of hardware scan phase before using software scan phase. There are presently only two recommended uses of Software Scan Phase:

Add Software Scan Phase if Hardware Scan Phase = 254 (or 0) is insufficient to even coarsely optimize image alignment
Add small amounts of Software Scan Phase to fine-tune the image alignment, if Hardware Scan Phase adjustment proves too coarse

However, for legacy Thor systems without hardware phase adjustment capability:

Hardware Scan Phase value has no effect; Software Scan Phase should be used exclusively.
It generally is NOT possible to optimally adjust Software Scan Phase (alone) at all combinations of , , and # Channels. Physical adjustment of scan phase within ECU electronics may be required to allow optimal adjustment at particular set of imaging parameters.

Users are recommended to upgrade their Thor hardware to allow hardware scan phase adjustment, especially if doing work spanning a wide range of imaging parameters.

ScanImage 4.1 aims to minimize scan phase adjustment required when changing imaging parameters:

ScanImage stores the last Hardware Scan Phase value set at each . Thus value need only be optimized once for each .
- For values without stored Hardware Scan Phase, last-set value at closest is used to minimize adjustment needed.
ScanImage stores last Software Scan Phase value set at each triad of (, , # acquiring channels).
Thus value need only be optimized once for each set of parameters.
- When or # Acquiring Channels are adjusted to value without stored Software Scan Phase, last-set value at current is used, to minimize amount of adjustment needed.
  
  values stored by SI 4.1 persist across ScanImage sessions (i.e. are stored in the ScanImage installation folder)
  For values without stored Software Scan Phase, value is always reset to 0. This reinforces that Hardware Scan Phase should be preferred to Software Scan Phase adjustment (because it is less sensitive to imaging parameters).

For Resonant Scanning, dwell time at each image pixel varies sinusoidally across the scanned field, with dwell time increasing towards the field edges where the scanner is accelerating/decelerating.

: Specify temporal fraction of each that Beam Modulation signal (Pockels) transmits excitation beam (if beam modulation is enabled). Increasing value also increase the mean pixel time and the (max/min) pixel time ratio.

: (Read-only) Fraction of full angular (spatial) scan range, at given , spanned by scanner during specified .

: Mean time, in ns, scanner dwells at each pixel for each image line.

:Ratio of pixel dwell time at edge (max) to center (min) of scanned field. Signal-to-noise ratio is increased at field edges; excitation exposure (i.e. potential photodamage/photobleaching) is also increase at edges.

If Beam Modulation (Pockels) is enabled, image will appear black or darker in vertical stripes at horizontal field edges, outside of the specified

: Finite value allows data from long acquisitions to be 'chunked' into several smaller files. Values specifies number of frames to log to each file; when this value is reached, ScanImage creates new file for logging subsequent frames. Disable file 'chunking' by setting value to Inf (default).
When file-chunking is enabled, ScanImage appends three-digit number (e.g. 001,002, etc) to filename, following an underscore.

: Locks to match set on MAIN CONTROLS. This is useful to force one file per slice, during stack acquisitions (i.e. where > 1).

: Enables logging data to disk during GRAB/LOOP acquisitions.

: If selected, beam modulation (Pockels) signal is generated, synchronized to each scanner period, that maximally attenuates the excitation beam outside of the specified . Power is at level specified in POWER CONTROLS

: If flyback blanking is enabled, specifies time (in us) by which transmission time during each scanned line should be increased beyond specified , e.g. to allow for possible modulation settling time, etc.

Beam modulation (Pockels) capability must be enabled in Machine Data File to allow flyback blanking feature. Otherwise power level is constant throughout each line (including long dwell time at field edges, which may cause photodamage/photobleaching issues).

Child pages

Configuration (r4.1)