iPSC/SYTO24/PhalloidinAF568 on 96-well plate; computational quantitative phase.
Antony C Chan

@article{,
title= {iPSC/SYTO24/PhalloidinAF568 on 96-well plate; computational quantitative phase.},
journal= {},
author= {Antony C Chan},
year= {2019},
url= {http://dx.doi.org/10.1038/s41598-019-47146-z},
abstract= {Complete dataset of the brightfield, darkfield, digital quantitative phase, and widefield fluorescence z-stack images of iPSC culture on the 96-well plate, captured by the Caltech parallel ptychographic imaging system (codename: 96 Eyes). The cell culture is stained with SYTO24 and PhalloidinAF568 for the proof of concept.

Also attached are the preview images in PNG format, as well as a minimal Python code to decode the raw data files.

Published in: A.C.S. Chan, J Kim, A Pan, H Xu, D Nojima, C Hale, S Wang, C Yang, "Parallel Fourier ptychographic microscopy for high-throughput screening with 96 cameras (96 Eyes)" Scientific Reports 9, 11114 (2019). http://dx.doi.org/10.1038/s41598-019-47146-z

Preprint: https://www.biorxiv.org/content/10.1101/547265v2

It is recommend that the raw pixels to be decoded on demand; otherwise it is not practical to load all >20GB data to computer memory just to crop the images later. Read the attached Python script `decoded.py` to learn how to select the region of interest (ROI) in-place to reduce the disk read/write time.

For Matlab users, on-demand pixel readout can be done with the `h5read` function. Try out the following pseudo-code, and debug accordingly to read all FPM raw pixels.

```matlab
fpm_raw = h5read('path/to/filename.h5', '/imlow', [1,1,well_id, 1], [512, 512, 1, 49]);
```

Reference implementation of the Fourier Ptychographic microscopy (FPM) phase-channel reconstruction algorithm, written in Halide the 4th generation coding language, will be published at:
https://github.com/antonysigma/fpm-96eyes-pipeline

},
keywords= {quantitative phase, 96 wells, high-throughput screening, iPSC, Fourier Ptychography, FPM, fluorescence},
terms= {Copyright (c) 2019, Antony C. S. Chan and Changhuei Yang
California Institute of Technology
Pasadena, CA, USA.

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}