Signal-to-Noise Visualization Mode

The Signal-to-Noise Ratio (SNR) Visualization Mode is designed to help users assess the quality of their images by visualizing the signal-to-noise ratio in real-time. This mode is particularly useful for identifying areas of high and low signal quality, which is helpful when aligning a microscope or when working with low-light conditions.

In the future, we will provide a method to acquire the offset and variance maps directly from within navigate. For now, users will need to provide these maps manually using commercial software provided by the camera manufacturer or by using custom scripts.

Acquiring Offset and Variance Maps

In general, it is a good idea to acquire the data used to derive the offset and variance maps at a similar exposure time as the one used for imaging. To calculate the offset and variance maps, users can follow these general steps:

  1. Capture Dark Frames: With the camera lens cap on, capture a series of dark frames (e.g., 1000 frames). These frames will be used to calculate the offset map.

  2. Calculate the Offset Map: Compute the minimum of the dark frames to create the offset map. This map represents the baseline signal level of the camera.

  3. Calculate the Variance Map: Compute the variance of the dark frames to create the variance map. This map represents the noise characteristics of the camera.

  4. Save the Maps: Save the offset and variance maps as tiff images in a folder titled camera_maps in navigate’s home directory.

    • For Windows-based users: C:\AppData\Local\.navigate\camera_maps\.

    • For Linux and MacOS users: /home/<username>/.navigate/camera_maps/.

    • The files should be named as <camera_serial_number>_off.tiff and <camera_serial_number>_var.tiff, where <camera_serial_number> is the serial number of the camera being used. By providing the serial number, users can easily switch between different cameras without needing to reconfigure the settings each time.

  5. Launch navigate: Next time you launch navigate, it will automatically detect the presence of the offset and variance maps in the specified directory and provide the appropriate options to enable the SNR visualization mode.