Program for selecting brain regions in stacks and saving their descriptors to file written in python using qt5.

The program allows loading 8, 16 and 32-bit grayscale and RGB(A) stacks (currently only tiff-stacks are supported). Regions can be named and selected in indivdual slices of the stack. To aid in segmenting, regions can be copied between consecutive slices.

The program allows adjusting the scaling and offset of the visualized images for easier visualization of underlying structure.

All segmentations can be saved from the user interface to hdf5 files. Saving/loading of regions outside of the RegionSelector program is easily done using the RegionContainer class in utilities.py. Otherwise information can be loaded by parsing the file structure listed below.

Keys are listed in italics, groups in bold.

• RootNode
  • 1
    • positions 2D numpy.ndarray of vertex coordinates for region 1
    • region_name str with the name given to the region
    • z_index int with the z plane index of the region in the stack
  • 2
    • positions
    • ...

No installation except for python and dependencies is required (easiest is to install a scientific python distribution such as Anaconda). Simply copy all repository files into one folder and then run

python start_regionSelector.py

from the command line.

Python 3.x

Numpy

Scipy

Pillow

Qt5

PyQt5

Pyqtgraph

h5py

Tested on Windows and OsX with python 3.5 and 3.6