SLICE Light Sheet controls
Purpose
Use the SLICE Light Sheet panel to enable the light sheets and adjust illumination settings.
The controls in the SLICE Light Sheet panel are used to optimize the illumination of the image by enabling a light sheet, choosing a color channel, and adjusting settings, such as the excitation intensity, duty cycle (i.e., the number of light sheets that scan the specimen per second), and offset. The offset is used to match the Z position of the light sheet to the current focal plane of the detection objective in order to achieve a sharp image. The offset will need to be adjusted frequently as you navigate to different focus positions in the specimen with the software joystick.
Best practices
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Determine the illumination settings in the SLICE Light Sheet panel that provide good illumination of the tissue with minimal or negligent photobleaching. To do this, you will primarily adjust the Excitation slider and the Duty cycle for each color channel to be imaged.
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Use the Camera Histogram and Camera Settings to optimize visualization.
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To keep the live image in focus, you may need to frequently adjust the Offset slider for the active light sheet(s) in the SLICE Light Sheet panel as you move the to stage to different locations in the sample.
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You can illuminate the sample with one or both light sheets (left and right) throughout the tissue scanning/imaging process. The approaches have a trade-off between minimizing imaging artifacts and achieving maximum resolution. Illuminating with both light sheets together helps reduce striping or banding artifacts that represent shadows cast by opaque material in the sample; this is common in light-sheet microscopy of cleared tissue and leads to signal loss in the horizontal direction. The SLICE system can mitigate such permanent signal loss by providing complementary illumination from opposite directions and can correct striping-pattern artifacts using a destriping algorithm. While differences in scattering and attenuation between the two light sheets may slightly degrade resolution, in well-cleared samples, the reduction in striping artifacts generally outweighs this minimal change in resolution.
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Save your settings to the multichannel control window
Once you have optimized all settings for a specific color channel save them to the Multichannel Control window. Whenever you switch channels in the multichannel control window, BrightSLICE will automatically switch all settings to the most recently saved values for that color.
Light sheet panel functions
Emission Filter
Emission Filter: Shows which filter is currently in position. The dropdown menu contains the filter for each color channel, and a neutral density filter. The emission filter will automatically switch to match the channel selected in the Multichannel Control window and to the neutral density filter when you start the SLICE alignment workflow. You can also manually select a filter in the dropdown menu.
Light Sheets
Click to turn the left or right light sheet on/off. When enabled, the indicator will be green. 
Enable automatic switching from the one light sheet to the other during an image acquisition.
Open the Split Sheet Configuration window to set a split threshold position where the switch from one light sheet to the other will take place when Enable Split is active.
Unlike all other settings, a split sheet configuration cannot be saved to the color in the Multichannel control window.
Excitation
Click next to Red, Green, or Blue to turn on the excitation for that color. When on, the indicator light will be white. 
Use the sliders, or type in a value to change the excitation intensity percentage.
For all sliders, click the arrows to move 1 unit at a time, click on the slider bar to move 10 units at a time, or drag the slider to dynamically adjust the value.
Right matches left checkbox:
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When checked, any changes to the excitation intensity percentage will be applied to both light sheets.
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When unchecked, left and right excitation controls will be separated and the Excitation Right settings will appear below the Right Sheet Controls. Changing the excitation value for one light sheet will not be applied to the other.
/ Toggle to turn off the current excitation/turn on the most recent excitation.
Left sheet controls, Right sheet controls
Use the sliders, or type in values to adjust the light sheet illumination.
Height: Set the height of the light sheet. We recommend a height of 2 which will cover 160% of the field of view.
Duty: Increase/decrease the duty cycle, which is the number light sheets that scan the specimen per second. We recommend a duty cycle of 720.
Center: Move the light sheet vertically to center it in the field of view.
Offset: Adjust the light sheet so it aligns with the current focal plane of the detection objective. The offset will need to be adjusted frequently as you navigate around the tissue specimen to achieve a sharp image.
Refractive Index (RI) compensation mapping enables you to record the proper offset position at different locations of the tissue sample and an RI compensation map is required for acquiring a Tissue Scan.
Stage
Move the stage up and out of the oil chamber in order to remove or attach a specimen cuvette to the stage.
Submerge a specimen cuvette into the oil chamber and position it for imaging.
Open and close the software joystick that you use to move the stage.