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Is deltascope right for you?

deltascope may be able to help you if:

  • your data consists of a set of 3D image stacks
  • your data contains a clear structure and shape that has consistent gross morphology between control and experimental samples
  • you want to identify extreme or subtle differences in the structure between your experimental groups
  • you have up to 4 different channels to compare

deltascope cannot help if:

  • your data was collected using cryosections that need to be aligned after imaging
  • your experiment changes the gross anatomy of the structure between control and experimental samples


deltascope can be installed using pip, Python’s package installer. Some deltascope dependencies are not available through pip, so we recommend that you install Anaconda which automatically includes and installs the remaining dependencies. See Setting up a Python environment for more details.

$ pip install deltascope


If you are unfamiliar with the command line, check out this tutorial. Additional resources regarding the command line are available here.


Packages required for deltascope depend on Visual C++ Build Tools, which can be downloaded at build tools.

Setting up a Python environment

If you’re new to scientific computing with Python, we recommend that you install Anaconda to manage your Python installation. Anaconda is a framework for scientific computing with Python that will install important packages (numpy, scipy, and matplotlib).


deltascope is written in Python 3, and requires the installation the Python 3 version of Anaconda.