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ImageJ-Fiji Quick Tip #1: Convert images as a batch

Keeping the raw format (e.g. nd2, lif, czi, oib, etc.) for your microscopy images is recommended to keep important acquisition information, such as pixel size, etc. However, you might need to convert them all at some point. Here is a quick tutorial post on how to do this as a batch in ImageJ / Fiji.


  • ImageJ users: you need the Bio-Formats plugin to read several raw formats. To know if you need it, a quick test is to open one image and see if it opens successfully. In any case, downloading the "Bio-Formats Package" jar file and putting it in your \ImageJ\plugins\ folder to replace the existing one is always a good thing.

  • Fiji users: go to menu "Help > Update" to ensure your Bio-Formats version is up-to-date.

No-code Version

For simple conversion to .tif files, follow these steps:

  1. Open ImageJ or Fiji

  2. Go to menu "Process > Batch > Convert..."

  3. Choose the input folder where your files are, and also choose an output one

  4. Keep all options as default, except "Read images using Bio-Formats" that you can check

  5. Press "Convert" and enjoy your new images

Spicy Version = add some processing steps

As you quickly noticed, you have some nice options to add some processing steps during that conversion in the previous dialog window. You can add more steps or just different ones by using the menu: