de.mdc-berlin / mbv_find-points-3d-from-2d / 0.1.0
macrophage-brain-vasculature find 3D points from 2D annotations solution
A solution for finding 3D coordinates from 2D annotations with respect to a target image
Usage instructionsPlease 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 (https://album.solutions)[https://album.solutions], 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.