# MicroscPSF-Matlab

**Repository Path**: liujin123time/MicroscPSF-Matlab

## Basic Information

- **Project Name**: MicroscPSF-Matlab
- **Description**: Fast and Accurate 3D PSF Computation for Fluorescence Microscopy
- **Primary Language**: Unknown
- **License**: MIT
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2020-08-18
- **Last Updated**: 2020-12-19

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

Fast and Accurate Three-Dimensional Point Spread Function Computation for Fluorescence Microscopy
=============
[J. Li](http://www.ee.cuhk.edu.hk/~jzli/), [F. Xue](https://www.researchgate.net/profile/Feng_Xue17) and [T. Blu](http://www.ee.cuhk.edu.hk/~tblu/monsite/phps/index.php), _J. Opt. Soc. Am. A_, 34(6), pp. 1029-1034, 2017.

This set of codes is a fast approximation of 3D PSF model in fluorescernce microscopy, based on Gibson-Lanni model. See [the page](http://www.ee.cuhk.edu.hk/~jzli/MicroscPSF) for details.

**Fast approximation** Current approximation can be 498 times faster than the state-of-the-art tool [PSF Generator](http://bigwww.epfl.ch/algorithms/psfgenerator/) for size 511x511x255. 
    Note the `PSF Generator` uses Java language with mult-threading, while the proposed uses pure Matlab without any compiled routine.


Usage of the Proposed Method
-----------

If the parameters of the microscope are not assigned, default setting will be loaded, see MicroscPSF for details.

```
params.size = [256 256 128];
tic;
PSF = MicroPSF(params);
toc
```
GUI
-----------
![GUI of MicroscPSF](GUI/screenshot.png?raw=true "GUI")

Even faster?
-------

The last interpolation step is implementated using mex files, which reduce the time cost 50%.

```
cd Utilities
mex transformation.cpp
```

```
params.size = [256 256 128];
params.fastcom = 1;
tic;
PSF = MicroPSF(params);
toc
```

System Tested
-----------

Mac | |
--- | --- |
`MATLAB R2016a` | `MATLAB R2015b` |


Update log
-----------
- (04 May, 2017) Add mex implementation, the speed is further improved 2 times!
- (28 Dec, 2016) Refined basis functions. 
- (09 Oct, 2016) Optimized code, the speed has been improved 10 times faster!

Related
-----------

* Matlab code: https://github.com/hijizhou/MicroscPSF-Matlab.

* ImageJ plugin: https://github.com/hijizhou/MicroscPSF-ImageJ.

* Icy plugin: https://github.com/hijizhou/MicroscPSF-Icy.

* Python code (by [Dr. Kyle Douglass](http://kmdouglass.github.io/)): http://kmdouglass.github.io/posts/implementing-a-fast-gibson-lanni-psf-solver-in-python.html

Acknowledgement
-----------
[PSFgenerator](http://bigwww.epfl.ch/algorithms/psfgenerator/)

License
-----------
Copyright (c) 2017, Jizhou Li, Feng Xue and Thierry Blu

The source code is released under the [MIT license](https://opensource.org/licenses/MIT).