Save/ Save as image stack

Purpose

Save a multiplane image—an image that include multiple Z-planes

Procedure and options for saving your image stack

  1. Go to 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.

    • 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.

  2. Click the Image Stack button.

    • From File > Save, clicking Image Stack saves the file and returns you to the previous NeuroInfo view.

    • From File > Save As, clicking Image Stack opens the Image Stack Save As window. Choose options and save or Export as described in the next step.

  3. In the Image Stack Save As window, choose options and save or export the image stack as follows:

    1. Navigate to the desired location for the file and type in a File Name.

    2. (optional) Choose from the following options:

      • Save/Export 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 NeuroInfo. 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 only and break its link to any associated data file.

        When checked, the Save button changes to an Export button.

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

        • This enables selection of additional Image Detail [or Stack Save Options] options.

      • Stack Save 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.

        • 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.

    3. Click the Save or Export button to save/export the file and close the dialog box.

See Image Stack overview