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Remove frst and Jupyter preview of DOG from PiSCAT
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Houman.M_Dastjerdi committed Dec 1, 2023
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17 changes: 6 additions & 11 deletions docs/Tutorial4/Tutorial4.md
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Expand Up @@ -119,24 +119,19 @@ RVideo_PN, _ = DRA_PN.differential_rolling(FFT_flag=False)
## Localization of proteins:
In this section, we directly work with the dynamic features that are remained in the DRA videos. As mentioned earlier the system response of a wide-field microscope for weakly scattering objects can be well approximated with a 2D Gaussian function. There exist a variety of localization algorithms available in the localization toolbox of PiSCAT. Difference of Gaussian ([DoG](https://piscat.readthedocs.io/code_reference.html#piscat.Localization.PSFsExtraction.psf_detection)) algorithm, for example, is suitable to perform a very efficient localization of proteins with pixel precision particle localization [[1](https://iopscience.iop.org/article/10.1088/1361-6463/ac2f68)].

In the following cell, a DRA video is being processed with a suitable set of parameters. The minima and maxima of the sigma values for the DoG kernels are lower and upper limits of the point spread function (PSF) size (in pixels) that one expects once the microscope response function is approximated with a 2D Gaussian function. The sigma ratio and the threshold values in this cell are set with respect to the contrast of the particles we are seeking to detect. We begin this analysis by presenting an interactive PiSCAT class that enables us to tune the DoG detection parameter and visualizes the localized particles dynamically.
In the following cell, a DRA video is being processed with a suitable set of parameters.
The minima and maxima of the sigma values for the DoG kernels are lower and upper limits of the point
spread function (PSF) size (in pixels) that one expects once the microscope response function is approximated
with a 2D Gaussian function. The sigma ratio and the threshold values in this cell are set with respect to
the contrast of the particles we are seeking to detect.



```python
from piscat.Localization import particle_localization

PSF_l = particle_localization.PSFsExtraction(video=RVideo_PN)
PSFs = PSF_l.psf_detection_preview(function='dog',
min_sigma=1.6, max_sigma=1.8, sigma_ratio=1.1, threshold=8.5e-4,
overlap=0, mode='BOTH', frame_number=[600, 7380])
```

![](../Fig/tu4_vid2.png)

Once we get to a working set of parameters for our localization algorithm we run the detection algorithm for all the frames of the video.


```python
PSFs_dog = PSF_l.psf_detection(function='dog',
min_sigma=1.6, max_sigma=1.8, sigma_ratio=1.1, threshold=8e-4,
overlap=0, mode='BOTH')
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1 change: 0 additions & 1 deletion piscat/Localization/__init__.py
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@@ -1,6 +1,5 @@
from .data_handling import *
from .directional_intensity import *
from .frst import *
from .gaussian_2D_fit import *
from .localization_filtering import *
from .particle_localization import PSFsExtraction as PSFsExtraction
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50 changes: 0 additions & 50 deletions piscat/Localization/difference_of_gaussian.py

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284 changes: 0 additions & 284 deletions piscat/Localization/frst.py

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