nplocate 0.1.2

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 influences of the PSF, even after very detailed and completed deconvolution procedures.

To squeeze a bit more information out of these highly distorted data, I wrote this code to effectly "fit" the entire 3D image. This is done in a quite sloopy way. For a perfect fit, please take a look at the very well crafted peri project.

The idea

This is not a fully functional particle tracking package like trackpy or colloids or peri. 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.
5. The more particles we have, the merrier.

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.

Cite the code

Just tell people you used trackpy