Converting TIFF to OME-TIFF (using Bio Formats)

Learn to convert a TIFF stack ZIP file to an open source format (OME-TIFF) using the Bio-Formats command line tools:

  1. Download the TIFF stack ZIP file that you want to convert. For example, go to this dataset https://doi.org/10.25550/2E-DST8, scroll down to the “Imaging Data” section and click the EuTH12.5mm1.zip file to download to your computer.

  2. Unzip the downloaded file. This will create a folder in your computer containing the stack of TIFF files. For the example above, the name of this folder will be DMSO12.5mm1_head and under that folder you’ll see a sequence of 511 TIFF files named DMSO12.5mm1_80000.tif to DMSO12.5mm1_80510.tif.

  3. Download the Bio-Formats command line tools file (bftools.zip) from: https://bio-formats.readthedocs.io/en/stable/users/comlinetools/index.html.

  4. Unzip the bftools.zip file to a new folder in your computer. By default, this folder will be called bftools. (This zip file contains the bundled jar and you no longer need to download bioformats_package.jar separately.)

  5. Create a .pattern file: In the folder with the stack of TIFF files, create a text file called stack.pattern containing a single line informing the converting tool how the files should be grouped. For the example given above, the line in the pattern file will be: 
    DMSO12.5mm1_80<000-510>.tif

    The pattern file can have any name but must use the extension .pattern and must be in the same folder as the TIFF files. (For more information on pattern files please see https://docs.openmicroscopy.org/bio-formats/6.9.1/formats/pattern-file.html) )

  6. Open a Terminal window (in Mac OSX or Linux) or a CMD window (in Windows) and change your directory to the bftools folder and type the following command: 
     ./bfconvert  /Path_to_FB_DATA_DIRECTORY/DMSO12.5mm1_head/stack.pattern  /Path_to_FB_DATA_DIRECTORY/DMSO12.5mm1_head.ome.tif

    Where we assume the FB_DATA_DIRECTORY is the folder where you initially saved the ZIP file downloaded from FaceBase (e.g., EuTH12.5mm1.zip). The bfconvert tool will create the resulting OME-TIFF file in this same folder.

  7. This OME-TIFF file may be visualized with an open source viewer such as Fiji, which is available from https://imagej.net/software/fiji/downloads.