Spatial- and Fourier-domain ptychography for high throughput bio-imaging

Title:      Spatial and Fourier domain ptychography for high-throughput bio-imaging
Version:    1.0 
Copyright:  Shaowei Jiang, Pengming Song, Guoan Zheng, 2023
License:    Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International Public License

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If you use this code, please cite the following paper:
Shaowei Jiang, Pengming Song, Tianbo Wang, Liming Yang,Ruihai Wang, Chengfei Guo, Bin Feng, Andrew Maiden, and Guoan Zheng,
"Spatial and Fourier domain ptychography for high-throughput bio-imaging", Nature Protocols, 2023. 

For algorithmic details, please refer to our paper.

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How to use: 

Foruier-domain ptychography (FP)
1. Unpack the full package and install related softwares. 
   Refer to 'Materials for Procedure 1: Fourier-domain ptychography' and 'Procedure 1: Fourier-domain ptychography' sections in our paper for additional details (including version number and instructions). 
2. We provide 4 different FP experimental datasets. Please refer to 'Content in this package' section for additional details. 
3. Run FP_Recovery.m for FP image reconstruction. The reconstruction time for a tile of 256x256 dimensions, with 4-times padding, is ~2 seconds. Please refer to our paper for additional information. 

Spatial-domain coded ptychography (CP)
1. Unpack the full package and install related softwares. 
   Refer to 'Materials for Procedure 2: Spatial-domain coded ptychography' and 'Procedure 2: Spatial-domain coded ptychography' sections in our paper for additional details (including version number and instructions). 
2. We provide 3 different CP experimental datasets. Please refer to 'Content in this package' section for additional details. 
3. Run CP_Recovery.m for CP image reconstruction. The reconstruction time for raw images with 1024*1024 dimensions, with 3-times padding, is ~58 seconds. Please refer to our paper for additional information. 

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Content in this package: 
CP_HeLaCellCulture              Dataset and reconstruction code of HeLa cell sample for CP
CP_Immunohistochemistry         Dataset and reconstruction code of IHC stained sample for CP
CP_UnstainedCytologySmear       Dataset and reconstruction code of unstained cytology smear for CP
FP_Intestine_Aberrations        Dataset and reconstruction code of Intestine cancer sample for FP
FP_H&E_RGB                      Dataset (RGB) and reconstruction code of H&E stained sample for FP
FP_Immunohistochemistry_RGB     Dataset (RGB) and reconstruction code of IHC stained sample for FP
FP_Leukemia_RGB                 Dataset (RGB) and reconstruction code of Leukemia sample for FP

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License of using this package (refer to 'license.txt'): 

Creative Commons Attribution-NonCommercial-ShareAlike 4.0
International Public License

Any inclusion or other use of this package means acceptance of this license.