How to use plugin
After installation, a new menu Plugins-> BigTrace X.X.X should appear in your Fiji.
It has two commands.
For now, you will need the first one: Open 3D image.
It will start the plugin and display a dialog to select a file with the volumetric data.
In short, BigTrace supports 3D composite multicolor images/stacks + (optional) timelapse stored as:
- TIFF files;
- proprietary BioFormats readable formats (.lif/.czi etc);
- HDF5/XML BDV files.
In addition, there is an option for on-the-fly deskew of Zeiss LLS7 czi files.
If you have trouble/errors while loading your dataset, please read Input data page.
After choosing a file, the plugin should load the dataset and show two windows:
- BigVolumeViewer showing 3D volume rendering of the loaded image and
- a control panel of BigTrace.
Congratulations. To get started, proceed to essentials:
- Display and navigation page describing dataset browsing;
- Creating ROIs page that covers basics of working with 3D ROIs;
and advanced topics covered in:
- Panel Measure provides details on different measurements and volume extraction;
- Panel Animation for movies creation;
- Panel Tracking for timelapse analysis;
Johanna M. Dela Cruz made an excellent video introduction to BigTrace, see below.
But it does not include many recently added features,
so please refer to this documentation.
