de.mdc-berlin / mbv_find-points-3d-from-2d / 0.1.0

macrophage-brain-vasculature find 3D points from 2D annotations solution

Annotation of Macrophage signal intensities
A solution for finding 3D coordinates from 2D annotations with respect to a target image
Solution written by
Kyle Harrington
Jan Philipp Albrecht
License of solution
Apache v2


csv filename (default value: PARAMETER_VALUE)
image filename (default value: PARAMETER_VALUE)
output csv filename (default value: PARAMETER_VALUE)
Gaussion blur sigma parameter. Usually >2. (default value: PARAMETER_VALUE)
debug mode (default: False) (default value: 0)

Usage instructions

Please follow this link for details on how to install and run this solution.

Find macrophage points in 3D from 2D solution

This macrophage-brain-vasculature solution finds the 3D coordinates of macrophage provided their coordinates of a two dimensional max projection.

How to run

Install album ([], download the solution file and install and then run it.


The solution has the following parameters:

  • input_filename: The input filename of the 4D image. The image should be a 4D image with the following dimensions:
    • 0: Channels
    • 1: x dimension
    • 2: y dimension
    • 3: z dimension
  • csv_filename: The csv file containing the 2D coordinates of the macrophages
  • output_filename: The output filename of the csv file containing the 3D coordinates of the macrophages
  • sigma: The sigma of the gaussian filter used to smooth the image
  • debug: If true, the intermediate results are shown

How it works

ImageJ is used to find the 3D coordinates of the macrophages. The 4D image is first smoothed using a gaussian filter. Then, the max projection is computed along the z dimension. The 2D coordinates of the macrophages are then used to find the 3D coordinates of the macrophages. The 3D coordinates are then added to the input csv file.