nplocate 0.1.0

Python tools to locate nano particles from confocal microscope images

Locate Nano Particles

What is this

nplocate is a custom script I wrote to locate very tiny particles from a confocal image. These images often suffered from extreme influence of the PSF, even after very detailed and completed deconvolution.

To squeeze a bit more information out of these highly distorted data, I wrote this code to effectly "fit" entire 3D image.

The idea

This is not a fully functional particle tracking package like trackpy or colloids. Instead, think of nplocate as an extension of current tracking packages.

The logic behind the code is quite simple. The arguments are,

1. It is easy to find some particles, even in a highly distorted image.
2. If we know the locations of some particles ({r}), we can measure their average shape (S).
3. With {r} and S, we can simulate a "fake image"
4. We can find previously unfound particles in the difference between the real image and fake image.

Installing the code

The simplest way is

pip install nplocate

You can also download this repository, and use the following command to install the code

pip install .

Using the code

There are some notebooks in the folder example that introduced how to use this package, along with trackpy.