Single Image
GTree trace module automatically provides the initial reconstruction of the local neuronal population, and then the user can edit the reconstruction result under the edit module(see User Manual section 3.6 for editing details).
Note: In single-image mode, image-level is useless and set as 1, which means the original image.
Import image stack: Click "OpenImage" under the file menu or "OpenImage" button on the tool bar. An "OpenImage" dialog will appear. Click the “open” button in the red square shown as below to import image stack (8-bit or 16-bit gray-scale, “.tif” format).
Note 1: For best visualizing, the size of the image stack should be no more than 2000 voxel in each dimension (x, y and z).
Note 2: The video memory of the user’s computer determines the maximum image size that can be imported and visualized.
Fig.1
Input the corresponding image resolution, then click the “accept” button.
Note: the image resolution is determined by the imaging system you applied to acquire image stacks.
Fig.2
The imported image stack can be visualized, which is shown below.
Fig.3
If there are somas, localize somas automatically or manually.(see Soma Localization).
Modify the binary threshold under "NeuroGPS" panel and click the "Preview" button. Check whether the binary segmentation result is best.
Automatic reconstruction: Click on “NGTree” button in the tool bar, and then Click on “ 
” button in the red square shown below.
Fig.4
The automatic neuron tracing results are shown below.
Fig.5
Although there is no soma, tracing operation can still be processed. The parameters under panel "NeuroGPS" in the left of GTree, control the location of soma and tracing of a single image. The functions of the parameters can be seen in the user manual https://github.com/GTreeSoftware/GTree/wiki/User-Manual .
