https://github.com/esoubies/ma-tirf_reconstruction

Multi-angle total internal reflection fluorescence microscopy (MA-TIRF) reconstruction algorithm which jointly performs volume reconstruction, deconvolution, and background estimation.
https://github.com/esoubies/ma-tirf_reconstruction

Last synced: about 1 month ago
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Multi-angle total internal reflection fluorescence microscopy (MA-TIRF) reconstruction algorithm which jointly performs volume reconstruction, deconvolution, and background estimation.

• Host: GitHub
• URL: https://github.com/esoubies/ma-tirf_reconstruction
• Owner: esoubies
• Created: 2018-11-21T07:17:10.000Z (about 6 years ago)
• Default Branch: master
• Last Pushed: 2021-04-28T17:17:57.000Z (over 3 years ago)
• Last Synced: 2023-10-19T19:49:36.690Z (over 1 year ago)
• Language: MATLAB
• Homepage:
• Size: 3.1 MB
• Stars: 1
• Watchers: 1
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# MA-TIRF_Reconstruction

## Description

Multi-angle total internal reflection fluorescence microscopy (MA-TIRFM) reconstruction algorithm which jointly performs volume reconstruction, deconvolution, and background estimation. More details can be found in the following papers:

Nanometric Axial Resolution of Fibronectin Assembly Units Achieved with an Efficient Reconstruction Approach for Multi-Angle-TIRF Microscopy.

Scientific Reports, 9-1, 2019.  


Emmanuel Soubies, Agata Radwanska, Dominique Grall, Laure Blanc-Féraud, Ellen Van Obberghen-Schilling, and Sébastien Schaub.

Improving 3D MA-TIRF Reconstruction with Deconvolution and Background Estimation. 

Proc. ISBI, 2019. 


Emmanuel Soubies, Laure Blanc-Féraud, Sébastien Schaub, Ellen Van Obberghen-Schilling.





 


   Left: MA-TIRF acquisitions. Right: Color-coded depth representation of the reconstructed volume (0--300nm).



## Requirements

The code requires the GlobalBioIm library v1.1.2 (or more recent releases)  https://biomedical-imaging-group.github.io/GlobalBioIm/

## Repository content

* main function **RecTIRF.m** 

* function **TIRF_matrix.m** which creates the MA-TIRF matrix given physical parameters

* function **OptiADMMtirf.m** : ADMM class derived from the OptiADMM class of GlobalBioIm

* function **getColorCodedDepthFig.m** which generates the color-coded depth representation of the reconstructed image

* folder **Example** containing a simple example of use in **Script.m**