Combine 2D images into a 3D stack

Overview

The Combine 2D Images into a 3D Stack mode converts a 2D image series into a 3D image stack. Image stacks can be converted to JPEG2000 and OME tiff image formats, or both.

Example: Convert a series of 2D tiff images into an image stack in JPEG 2000 and/or OME tiff format.

See the list of compatible file formats.

The procedure includes 4 steps (click steps to jump to procedure details):

  1. Choose conversion settings
  2. Indicate files to be converted and the destination for the converted files
  3. View and/or edit metadata
  4. Click to convert the files

Procedure

  1. Click the button, Combine 2D Images into a 3D stack to choose file-conversion settings.

    1. Save Format: Choose the format for your output image file:

      • JPEG 2000: file extension ".jpx" (learn more about the format)
      • OME TIFF: file extension ".tif" (learn more about the format)
      • Both: saves as both file types

    2. JPEG 2000 Compression: If you chose JPEG 2000 or Both, choose the compression settings for the JPEG 2000 image; file conversion to this format can be compressed (lossy) or uncompressed (lossless).

      • It is recommended to select lossless compression when converting images approximately 1 GB or less in size, or when converting a JPEG.
      • If you choose Lossy compression, indicate the compression ratio desired.

    3. Indicate the Z Plane Spacing, or z-step, in µm, for the 3D image stack.

    4. Advanced: Other available options

      • Skip .jp2 (JPEG 2000) files
      • Force incremental saving
      • Require metadata entry before saving: this option is selected by default

  2. Click Next to select source file(s) and indicate the output destination.

    Images selected or dragged and dropped together will be combined into one 3D stack. Multiple 3D stacks may be created by selecting or dragging and dropping each series of images separately.in the format(s) selected in Step 2.3.

    1. Select the image(s) to combine into 3D stacks via drag and drop or navigating and selecting as described below:

      • Drag and drop: select images as a group and drag into the Microfile+ window together. To create multiple stacks, drag and drop the files in groups.

      • Click the Load files.... button, navigate to the location of the file(s) you want to convert, select the group of images to combine into a stack, and press Open.

        To create multiple stacks, repeat the file-group selection process.

      • Single images brought into the image selection plane will be converted to a single plane image.
      • The file(s) will appear as groups in the Microfile+ window.
      • To remove a file from the conversion window, select the file and press Remove Selected.

    2. Destination for image stack(s) after conversion:

      • By default, image stack(s) are saved to the same location as the original(s).

      • To select a different location for all stacks in the window, click the Select Output... button, navigate to the destination folder, and click Select Folder.

      • To select a different location for individual stacks in the window, click the Save button next to the file name, navigate to the destination folder, click Open, and click Save.

  3. Click Show Metadata to view/edit metadata.

    • The Show Metadata button is in the lower left-hand corner of the window.
    • Click to select files in the conversion window and view the metadata for that file stack in the Metadata Generation panel on the right.

    • The status of metadata completion is indicated next to each stack:

      • Green check mark indicates that critical metadata is sufficient.
      • Red X indicates that critical metadata is missing. Click the file name and the critical metadata fields are highlighted in yellow. Pink boxes indicate fields that lack information. Double-click to enter metadata.

    Learn more about entering/modifying metadata here.

    See the Metadata Glossary for more information on each metadata field

  4. Click Convert to begin the conversion process.

    • If there is a file with the same name in the output directory, the "File Already Exists" dialog opens. Click yes to proceed and “converted” will be added to the end of the file name to distinguish the new file conversion process.