The 2D Frame tab allows the user to adjust basic scan parameters for image display and acquisition.
|A||Field of View||These values are calibrated for each objective used on the system and automatically adjust with the zoom factor.|
|B||no. of frames to acquire||The number of frames that will be saved in next acquisition.|
|C||Frame Rate (frames/s)||Displays current frame rate|
|D||Scan Resolution||Contains pre-set Scan Resolutions*. Arbitrary resolutions in X are not possible with a resonant scanner.|
|E||ZOOM||Moving the slider allows the user to zoom in and out.
Please Note: this zoom is operates by adjusting the scan mirror angles and is distinct from digital zoom in the display window.
|F||Start Delay||Adjusts the timing delay between acquisition of the forward and reverse scans (bidirectional scanning) to remove comb artefacts.|
|G||start.delay.auto.correct||Clicking the green button activates the start delay auto correct feature, see below.|
|H||x.Correction||Shifts the displayed area relative to the mirror phase to help adjust for the x-mirror's motion profile.|
Please Note: 1024x resolutions are only available if using the NI5734 120MHz Digitizer and 1536x resolutions are only available if using the NI5751 40MHz Digitizer due to data sampling limitations.
Start Delay Autocorrect
The Start Delay Autocorrect feature automatically attempts to find the most appropriate start delay setting by using image features to line up the forward and reverse scan lines.
- Choose a PMT channel to make the adjustment
- Focus on a structured and contrasted area of the sample
- A moving average of at least 10 frames must be applied to improve the image quality
- Click the start.delay.autocorrect button
- Some adjustment may be needed if image features are not clear enough. If much worse, focus on a different area and try again
Start Delay Lookup Table
To avoid having to adjust the start delay every time you change a parameter; SciScan creates a look-up-table using the startdelayLUT_coMD.vi plugin. SciScan keeps track of the last used start-delay setting for a given combination of scan parameters (zoom, resolution, ect..) and saves it for the next time you use these settings. If you are using a set of parameters for the first time you will need to correctly set the start delay by either adjusting the start delay slider, or by using the Autocorrect feature as described above. Once it has been correctly set once, you should be able to switch back to these settings and the start delay should be remembered.
Posthoc Start Delay Correction
If tan image has been recorded with the incorrect start delay, this can be corrected posthoc in the RAW file using the posthoc start delay correction.vi. For information on how to correct the VI see the Posthoc Start Delay Correction page.
Resonant Scan Correction
Resonant mirrors move with a sinusoidal motion profile. As the mirror approaches it’s turn-around point the pixel dwell time remains constant but the mirror velocity decreases, giving the impression that the image becomes “stretched” at the edges. The two standard mechanisms employed to correct for the change in velocity are:
- Discarding affected portions of the image – SciScan discards the affected areas near the turning point of the mirror and only displays the central 512 pixels (66%) of the image.
- x.correction – The x.correction setting in SciScan allows you to shift the field of view relative to the mirror phase i.e. move the displayed area left or right. In order to display the most linear portion of the scan.
Another consequence of the sinusoidal change in velocity across the field is that a given volume of tissue near the mirror turning points will be exposed to laser excitation for longer periods of time compared to tissue at the center of the field of view. This may lead to photobleaching and photodamage.
To avoid adverse effects of laser overexposure during turn-around, SciScan offers a blanking module, which rapidly switches a Pockels Cell in order to attenuate the laser at the edges of the field.
Please see the Knowledge Base Article: Laser Intensity Control (Resonant) for more information on Blanking