The modelwfs from ivovellekoop

modelwfs's Introduction

"Model-based wavefront shaping microscopy"

Matlab scripts to generate all the data underlying the article "Model-based wavefront shaping microscopy" [ Correspondence to: [email protected]]

Comparison of Model-based wavefront shaping and feedback-based wavefront shaping

Running sequence:

Generate refractive index map from TPM intensity images.

(a) Run /refractive_index_mapping/ShearTPMimage.m for coverting the acquired TPM frames to actual size in micrometer.
```
Input file: Image from ScanImage (Here, eg. PDMS_diffuser_surface_1X512.tif) 
Output file: TPM_3D.m
```
(b) Run Refractive_Indexmap_3D.m to generate refractive index distribution.
```
Required input: TPM_3D from the previous step.
Output file: Sample properties (eg. n_sample, PDMS_thickness)
```
Run Model_WFS_PhaseConjugation.m for simulating light propagation through the PDMS diffuser to find correction wavefront.
```
Input: SampleProperties.m 
Output: SLMCorrection.m
```
Run feedback_optimization.m for finding the optimal wavefront.
```
Output: ideal_wavefront.m
```
Run WFScomparison.m for generating the Phase pattern on the SLM and compare the model-based wavefront shaping with feedback-based wavefront shaping.

Inputs: SLMCorrection and ideal_wavefront

Data Analysis codes:

ModelWFS_DataStitching.m is used to stitch 3D substacks to form a combined 3D stack.
ModelWFS_DataAnalysis.m - Generate maximum intensity projection. Compute mean intensity of the beads as a function of depth.
plotSLMpatterns: Generate SLM patterns at different depths. Four patterns corresponding to four depths are used in the paper.

Recommend Projects