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

# 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

## Arguments

## 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 (https://album.solutions)[https://album.solutions], download the solution file and install and then run it.

## Parameters

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.