Installation of javabridge on Windows (ValueError: numpy.ndarray size changed error)

[ElpadoCan]

Cell-ACDC on Windows automatically installs a pre-compiled version of javabridge when you first launch the module "0. Create data structure from microscopy file(s)...".

However, it doesn't seem to work on every Windows PC and you get the following error (see issue #9):

ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject

In this case, you need to install javabridge manually as follows:

1. Download and install Microsoft C++ Build Tools from here. IMPORTANT: make sure to select Desktop development with C++ when installing the C++ Build Tools. See screenshot below
2. Download and install Java Development Kit for Windows from here. Note: if you prefer to install Java directly from the Oracle website you can download it from here, but you will need to create an Oracle account
3. If you do not have git you need to install it from here
4. Open the Anaconda Prompt and activate the acdc environment
5. Uninstall javabdridge with the command pip uninstall -y javabridge
6. Install javabdridge with the command pip install git+https://github.com/SchmollerLab/python-javabridge-acdc

If you are still having issues, comment below, thanks!

Visual Studio Build Tools installation:

[jordanyx]

This solution worked for me, thank you!