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 ****************************************************************************** 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. ****************************************************************************** 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. ****************************************************************************** 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 ****************************************************************************** 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.