/cellshape-helper

Cellshape-helper provides the ability to convert 3D masks to point clouds.

Primary LanguagePythonBSD 3-Clause "New" or "Revised" LicenseBSD-3-Clause

Project Status: Active – The project has reached a stable, usable state and is being actively developed. Python Version PyPI Downloads Wheel Development Status Tests Coverage Status Code style: black

Cellshape logo by Matt De Vries

Cellshape-helper provides the ability to convert 3D masks to point clouds.

To install

pip install cellshape-helper

Basic Usage

import cellshape_helper as helper


PATH_TO_TIF_FILES = "path/to/tif/files/"
PATH_TO_SAVE_MESH = "path/to/save/mesh/files/"
PATH_TO_SAVE_PC = "path/to/save/pointcloud/files/"
NUM_POINTS = 2048

helper.tif_to_pc_directory(PATH_TO_TIF_FILES, 
                           PATH_TO_SAVE_MESH, 
                           PATH_TO_SAVE_PC, 
                           NUM_POINTS)

Parameters

  • PATH_TO_TIF_FILES: str.
    The path to you binary masks of cells or nuclei.
  • PATH_TO_SAVE_MESH: str.
    The path where you want to save the mesh objects to.
  • PATH_TO_SAVE_PC: str.
    The path where you want to save your point clouds to.
  • NUM_POINTS: str.
    The number of points to sample from the mesh object when creating a point cloud.