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