A python program (scripts) for viewing and inspecting of volumetric data and neuron morphology data using VTK with 3D computer graphics experience.

Supported data format:

TIFF and IMS (HDF5) for volumetric data.
SWC for neuron morphology data.

Typical use cases:

Viewing the data with your favorite angle or perspective.
Load and inspect SWC files, relevant information will be shown for clicked node.
Run custom scripts (plugin) to analyze or alter the data, then seeing the result right away.
Press F2 to go to command line mode for prototyping, i.e. type swcs.line_width = 2 to set line width of all SWCs.
Work with the source code for your own craft.

Features

Thanks to VTK, we can also view in stereo modes (binocular 3D), such as split the view port horizontal, red blue or interlaced.
Parallel loading of SWC files for speeding up work flow.
Example plugins for coloring SWC files, e.g. color by node depth.
Measure distance between selected points.
Facilities for easier work with SWCs, such as batch read / assignment.
Save the current scene (including view angle) to a file.
The plugin system can essentially let you do almost any modification to the program.
Customizable key bindings, through plugins/plugin.conf.json.

Demo

Installation

Install Python3

Linux

It is most likely already installed.
Windows

Try follow the official directive. Install the latest stable version is recommended (at the time of writing, it is 3.11.1). For greater compatibility and stability, try stable version of last minor version (such as 3.10.9).

Install dependencies

Use pip

pip install vtk tifffile h5py scipy IPython joblib

Or

pip install -r requirements.txt

or if you are in mainland China and need a faster pip download speed:

pip install -i https://pypi.tuna.tsinghua.edu.cn/simple -r requirements.txt

It is recommended to use the latest stable version of vtk. e.g. vtk 8.2 has a known bug affects this program, and it is fixed in vtk 9.2.

pip install --upgrade vtk

Download code

Use git

git clone <url>

For example <url> could be:

https://github.com/bewantbe/SimpleVolumeViewer.git

Or, download current version

Click the "Download ZIP".

Unzip it somewhere, there is no need to "install" it.

Running

In command line (terminal) window

cd to where you put this repo, e.g.:

cd SimpleVolumeViewer

Run:

python3 -m neu3dviewer

then drag-and-drop file(s) to the GUI.

Or, with options:

python3 -m neu3dviewer <options>

e.g. to load all SWCs in a directory:

python3 -m neu3dviewer --swc_dir brain_data\v1.6.2\swc_registered_low\

See python3 -m neu3dviewer --help for full list of options.
Use the "Windows" way:

Double click the executable SimpleVolumeViewer/bin/neu3dviewer.bat the drag-and-drop.

Or create/use a shortcut like SimpleVolumeViewer/bin/neu3dviewer_py310. It is recommended to alter the compatibility option for HiDPI to fix the blur problem. e.g. in properties of the shortcut open Compatibility tab, -> Change high DPI settings -> Override high DPI scaling behavior. Scaling performed by: Application.
To get help

python3 -m neu3dviewer --help

Or, press h key in the GUI.

Developer notes

Reload a modified module during running

Method 1 example:

    import sys
    import importlib
    importlib.reload(sys.modules['neu3dviewer.data_loader'])
    from neu3dviewer.data_loader import *
    #now neu3dviewer.data_loader get refreshed

Method 2 example (need to run in ipython):

    # Ref. https://ipython.readthedocs.io/en/stable/config/extensions/autoreload.html
    # at the start of a working session. (now this step is automatically done when pressed F2)
    %reload_ext autoreload
    %autoreload 2

    # then work as usual, the imported objects will be updated
    from neu3dviewer.data_loader import *
    help(Struct)
    # modify class Struct, then it is different
    help(Struct)