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Convert large dataset to BDV format

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Eugene Katrukha edited this page Oct 7, 2024 · 2 revisions

To work with large datasets, exceeding the computer's memory (RAM) and GPU memory, they first need to be converted to BDV XML/HDF5 format. This will create the pyramidal data structure, so only blocks of required resolution will be loaded.
Here are some short instructions on how to do it.

  1. Open your file in FIJI as a Virtual stack.
  • If opening regular TIFFs, use File->Import->TIFF Virtual Stack command.
  • If opening proprietary files using BioFormat Importer, make sure to select "Use virtual stack" checkbox.
  1. Run the following command: Plugins->BigDataViewer->Export Current Image as XML/HDF5. Usually, default settings are fine.
    In the Export path box choose a destination folder and file name of the converted dataset. Click OK.
  2. It will usually take some time to export the data, follow the Log window update.
  3. Once "done" is displayed in the Log window, the export is finished and you can open your data in BigTrace.

Developed in Cell Biology group of Utrecht University.
Check out Updates history. The plugin and this wiki are under constant development.
E-mail for any questions, feedback, errors or suggestion or tag @ekatrukha at image.sc forum.

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