Convert large dataset to BDV format - ekatrukha/BigTrace GitHub Wiki
To work with large datasets, exceeding the computer's memory (RAM), they first need to be converted to BDV XML/HDF5 format. Here is a short instruction on how to do it.
- 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.
- 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. - It will usually take some time to export the data, follow the Log window update.
- Once "done" is displayed in the Log window, the export is finished and you can open your data in BigTrace.