Save /Save as

Procedure and Commands

  1. Go to File >

    • Save if you want to save updates to a file that has been previously saved and you do not want to update the file name or location. This will overwrite the original file.

    • Save As if you're saving a file for the first time or want to save a file with an updated name or location. This will not change the original file.

  2. Click the icon that corresponds to the type of file you want to save.

    Note that the list below includes commands found in both Save and Save As

Image: Save an image.
Image stack: Save multiplane images—images that include multiple Z-planes .

Current Plane: Save only the currently displayed plane in an image stack (multiplane image) .

  • (optional) Save as type drop-down menu:

    • MBF JPEG2000 is the default file type: we recommend it.

    • MBF JPEG2000 and MBF TIFF files can include high bit-depth pixel data (if present) and image-display adjustments you've made in BrightSLICE. Metadata about the image, such as the microscope hardware used, is also saved.

    • JPEG2000 file format offers smart compression that can result in a significant reduction in the amount of storage space needed, with minimal data loss.

    • TIFF file format is uncompressed.

  • Export the image file: Check the box to save (export) the image and break its link to any associated data file.

    • The original image-display information and any high bit depth data that were present are lost.

    • This enables selection of additional Image Detail options or Stack Save Options (described below).

    • When checked, Save changes to Export.

  • Image Detail options:

    • Save as individual channels [available for multiple color-channel images]: Saves each color-channel in the image as a separate file.

      The channel number is added to the end of the file name, e.g., "FileName_Ch01.jp2"

    • Save image color [available when you select Save as individual channels]: Saves the color information with each separate channel or stack.

  • Stack Save Options:

    • Same as Image details options, plus:

    • Save as a series of single image files: Save each image plane as a separate file.

      The plane is added to the end of the file name, e.g., "FileName_001.jp2" or "FileName_001_Ch01.jp2"

  • Compression (available when either JPEG2000 file type is selected): Use the slider to indicate the amount of file compression desired.

    File compression settings have a direct and significant impact on image file size. We carefully examined the effects of SLICEdata compression and identified an optimal compression range of 15–20:1, which reduces file size approximately 93% while preserving scientific validity (see our white paper, A Practical Guide to Selecting Compression Levels for 3D Light Sheet Fluorescent Microscopy Data). We recommend routinely applying 15–20:1 compression for both working files and long-term archiving. More aggressive compression ratios are possible but should be validated for each data type and analysis workflow by comparing to uncompressed or lightly compressed versions of the same data to confirm that fluorescence-intensity values are not meaningfully affected.

    The image below compares different wavelet based compression factors. The left panel shows raw uncompressed image. The middle panel shows 10:1 compression with JP2000 wavelet. The right panel shows 30:1 JP2000 wavelet compression. A 10:1 compression exhibits virtually no compression artifacts. At 30x, there are some minor artifacts and a slight reduction in dynamic range.

     

    Uncompressed 10:1 30:1