HERBS

A Python-based GUI for Histological E-data Registration in Brain Space

HERBS is an open source, extensible, intuitive and interactive software platform for image visualisation and image registration. Where the image registration is the process of identifying a spatial transformation that maps images to a template such that corresponding anatomical structures are optimally aligned, or in other words, a voxel-wise ‘correspondence’ is established between the images and template.

HERBS has been tested on Windows 10, MacOSx (Big Sur - Monterey), Linux (Kubuntu 18.04, Ubuntu 22.04 LTS), and as a python application, it should run in all environments supporting python 3.8.10-3.9.16 / 3.9.0 with PyQt5 >= 5.14.2 as a GUI framework. For details, please see HERBS CookBook or Tutorials(most recent update).

HERBS provides users:

• 2D and 3D visualisation of brain atlas volume data and arbitrary slicing.
• Image registration with interactive local elastic deformation methods in current version.
• 2D and 3D visualisation of user defined data.

Install

$ pip install herbs

Please install the newest version of HERBS.

Usage

import herbs
herbs.run_herbs()

After running the above scripts, a GUI window will pop up. Users can download atlas and upload images for further process,

For more information, please read HERBS CookBook (on going) or check the Tutorial folder for corresponding functionalities.

Atlas Storage

• Do not store Atlases inside HERBS folder.

When downloading Atlases, HERBS asks users to select the folder to store the atlas. Please choose a folder other than HERBS folder.

• Save different Atlas in different folders.

When downloading an atlas other than the one you already have, please store it in another folder.

Some Pre-Requirement Issues

• In order to run HERBS properly, 64 bit operating systems and 64 bit Python are required.

• 3D visualisation in HERBS depends on OpenGL, if you face to the problem that no OpenGL is installed on your machine, please see (https://www.opengl.org) to download and install accordingly.

• If you use MacOS and face to the problem of ImportError states that "Unable to load OpenGL package". Please try to find the OpenGL package folder from where you install all python packages in your enviroment, and go to OpenGL's child-folder "platform", open "ctypesloader.py", and change line

fullName = util.find_library( name )

to

fullName = '/System/Library/Frameworks/OpenGL.framework/OpenGL'

• For the current version of HERBS, Python is required to be installed. Please see (https://www.python.org) for downloading.

• If you would like to install HERBS through terminal, pip is required.

  • Check if pip is installed, pip --version or pip help.
  • Use python3 -m ensurepip for MacOS to install pip.
  • Use curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py to download requiring file for installing pip on Windows and python get-pip.py to install pip.
  • Please update pip to the newest version before installing HERBS.

• We strongly recommend users to use Python and install packages with virtual environment. For no-coders, we strongly recommend to use IDE to create environment at the moment. A desktop app of HERBS is on its way.

Some Dependencies Conflict Issues

• The initial of test of HERBS was carried on Windows 10 (one user claimed he had a Windows 11 before, but it turned out to be a Windows 10 at the end), MacOSx (Big Sur - Monterey) and Linux (Kubuntu 18.04, Ubuntu 22.04 LTS) with Python==3.8.10 and the corresponding dependencies listed in CookBook.

• The current tests showed that different version of Python accepts different versions of dependencies. For example, PyQt5 == 5.14.2 works when Python>=3.8.10 and PyQt5 >= 5.15.0 works when Python==3.9.

• HERBS depends on Numba and the valid version for Numba is highly depends on the version of Numpy. For example, Numba == 0.54 only works when Numpy <= 1.20 and Numba == 0.55 only works when Numpy <= 1.21 and so on.

• If you face to these kinds of problems, the easiest way to install HERBS is to create a new environment and install HERBS without previous installation of any dependencies.

Please report your issues: https://github.com/JingyiGF/HERBS/issues. Please have a good description (maybe a screenshot or an error message). Any feedback welcome!

Please feel free to start any discussion: https://github.com/JingyiGF/HERBS/discussions.

Finally

HERBS is 'always' in development, please check updates every time before you use it.

Hope this tool makes your amazing research life more tasty :-)