Camera Settings window

Purpose

Click Camera Settings on the Acquire ribbon to open the Camera Settings window.

Use the Camera Settings window to adjust the SLICE camera settings for each color channel to optimize image acquisition.

Click More Settings in the Camera Settings panel to access settings specific to the camera on your microscope system. For assistance with camera-specific settings, contact our Technical Services staff by completing the Request Support form.

Camera settings

Exposure

Exposure is the amount of time that the camera system collects light from the specimen on the microscope. Adjust the exposure using any of the following methods:

  • Increase or decrease the exposure time by moving the slider to the right or clicking arrows.

    The exposure time in milliseconds (ms) is displayed in the box.

  • Enter the desired exposure time in the box.

  • Click Automatic to set an automatic exposure-time based on the percent luminance shown in the box to the right. We recommend ~70% luminance in many cases; type the desired value into the box to change it.

Note that, with long exposure times, you will want to pause between movements of the stage to see the specimen—letting the camera "catch up." To avoid delays in viewing the live image when the stage is moving, set the exposure time to 50 ms or lower.

Gain

Increase the Gain slider to amplify the signal from the camera. Note, however, that both "true" signal and signal from noise are amplified as you increase gain.

  • Increase or decrease the gain by moving the slider to the right or clicking arrows.

  • We recommend setting the gain at 300–600 in many cases.

Other

More Settings: Click to open additional settings organized in tabs (General Settings and Binning and Cropping.

  • General Settings tab

    • The General Settings tab contains the same Exposure and Gain controls as on the main Camera Settings panel.

    • Reset Camera Used for trouble shooting camera issues. If you are having problems with the camera or live-camera feed, please contact our Technical Services staff .

  • Binning and Cropping tab

    • Binning: Select the number of pixels to bin (combine) from the dropdown menu. We recommend 2×2 binning in most cases. When "1" is selected, pixels are not binned.

      Pixel binning combines signal from adjacent pixels to effectively reduce exposure time and noise, while increasing dynamic range.

      We recommend associating pixel-binning with software lenses in BrightSLICE software. If that is not already set up on your SLICE system, follow this procedure to configure software lenses.

      Note that binning changes the scaling (pixels per micron).

      For more in depth information about binning and image compression, see our white paper (PDF) A Practical Guide to Selecting Compression Levels for 3D Light Sheet Fluorescent Microscopy Data.

    • Bit Depth: Bit depth specifies how much color information is available for each pixel in an image. More bits of information per pixel result in more available colors. Choose the desired bit depth from the dropdown menu.

    • Live crop: Use live crop to exclude areas of vignetting and image distortion from the edges of the field of view. You can manually enter the desired size and position values, but we recommend using the Configure Crop tool to set the size and position of the live crop.

      • X Centering: How many pixels the crop has been shifted in the X axis to center it in the viewing window.

      • Y Centering: How many pixels the crop has been shifted in the Y axis to center it in the viewing window.

      • Width: The width of the live crop in pixels.

      • Height: The height of the live crop in pixels.

      • Apply Crop Click to apply crop size and position values manually entered into the fields above.

      • Clear Crop Click to clear an active live crop. The cropping will be removed and the viewing area will display the entire field of view from the camera feed.

        Note that clearing a crop cannot be undone. To apply a live crop again, the crop will need to be reconfigured or position and size values will need to be manually entered.

      • Configure Crop Click to configure the size and position of the crop. See Live crop to learn more.

Notes and recommendations for adjusting camera settings

  • In fluorescence microscopy, it may be helpful to identify and focus on labeled structures using a relatively fast exposure time and boosting the signal through gain adjustments. Then, in order to capture a high-quality image, reduce the gain and increase the exposure time.

    For example, you have a dim fluorescence signal and need a (long) 1,000 ms exposure to see your labeled structure. To rapidly view the entire specimen and identify areas of interest from which you want to capture images, reduce the exposure time to ~50 ms and adjust the gain, to boost the signal (at the expense of quality). Once you have focused on a field of view, capture a good-quality image by increasing the exposure and reducing the gain.

  • Increasing binning can improve imaging speed and reduce image file size. We recommend using 2×2 binning (effective pixel size of 520 nm). Given that the lateral resolution of SLICE is 0.8–1.0 µm, 2×2 binning preserves most structural details while improving imaging speed and reducing data size. Using 3×3 binning (effective pixel size of 780 nm) can further increase speed and decrease file size, but may compromise your ability to capture the smallest structural features.