How to use plugin - ekatrukha/BigTrace GitHub Wiki

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;

Video tutorial

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.