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\citation{Kim2016}
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\@writefile{toc}{\contentsline {subsection}{Parallel FPM acquisition and reconstruction}{1}{section*.1}}
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\@writefile{lof}{\contentsline {figure}{\numberline {S1}{\ignorespaces {\bf  Parallel FPM acquisition and reconstruction process.}(a)~Timeline of plate image acquisition and reconstruction processes two consecutive plates. Since the reconstruction process can be done offline, the second plate can be loaded and imaged while the workstation is reconstructing the images of the first plate. (b)~and~(c)~Four (4) high-throughput frame grabbers streams raw images to the internal memory buffers of the workstation through the high speed links. (d)~Front view of the 96~Eyes hardware.\relax }}{2}{figure.caption.2}}
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\newlabel{fig:timeline}{{S1}{2}{{\bf Parallel FPM acquisition and reconstruction process.}(a)~Timeline of plate image acquisition and reconstruction processes two consecutive plates. Since the reconstruction process can be done offline, the second plate can be loaded and imaged while the workstation is reconstructing the images of the first plate. (b)~and~(c)~Four (4) high-throughput frame grabbers streams raw images to the internal memory buffers of the workstation through the high speed links. (d)~Front view of the 96~Eyes hardware.\relax }{figure.caption.2}{}}
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\citation{Yeh2015}
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\newlabel{fig:illumination-sequence}{{S2}{3}{{\bf Detailed illustration of the parallel illumination scheme of 96~Eyes.} The source-to-source separation is chosen to maximize the effective acquisition rate, as well as avoiding interference. This is made possible by making sure that only one single LED is responsible for brightfield illumination for any camera and for any time instance of ptychographic image acquisition. Inset: definition of symbols for LED position calibration.\relax }{figure.caption.3}{}}
\@writefile{toc}{\contentsline {subsection}{Speed improvement factor and the design criteria of the parallel illumination scheme}{3}{figure.caption.3}}
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\@writefile{toc}{\contentsline {subsection}{Modification to the Fourier ptychography phase retrieval algorithm}{3}{equation.Alph0.9}}
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\citation{Yeh2015}
\citation{Lu2016,Tian2015}
\citation{Pan2017}
\citation{Hou2018}
\citation{Tian2014}
\citation{Ou2014}
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\citation{Lu2016,Tian2015}
\citation{Widrow1961,Schuchman1964,Vanderkooy1984}
\citation{Roberts1962}
\citation{Balsam2012}
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\@writefile{toc}{\contentsline {paragraph}{Choice of adaptive step size for pupil recovery}{5}{figure.caption.5}}
\@writefile{lof}{\contentsline {figure}{\numberline {S3}{\ignorespaces {\bf  Particulates outside of the focal plane introduce background interference.} (a)~Phase component of the recovered complex wavefront, showing the the U2OS cell line almost buried in the phase fluctuation; (b)~phase image of dust particles on the underside of the well plate, reconstructed by digital refocusing of the recovered complex wavefront. (c)~Recovered phase component of system aberration; and (d)~pupil function used for digital refocusing.\relax }}{5}{figure.caption.4}}
\newlabel{fig:background-interference}{{S3}{5}{{\bf Particulates outside of the focal plane introduce background interference.} (a)~Phase component of the recovered complex wavefront, showing the the U2OS cell line almost buried in the phase fluctuation; (b)~phase image of dust particles on the underside of the well plate, reconstructed by digital refocusing of the recovered complex wavefront. (c)~Recovered phase component of system aberration; and (d)~pupil function used for digital refocusing.\relax }{figure.caption.4}{}}
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\@writefile{lof}{\contentsline {figure}{\numberline {S4}{\ignorespaces {\bf  Adaptive step size improves pupil function recovery.} (a)~Recovered phase component of pupil function with a constant step size, i.e.\ at $\beta =1$, compared to (b)~at $\beta = 10^{-6}.$ Symbols $(\rho _x, \rho _y)$ are the local coordinates of the pupil function. (c)~Comparison of reconstruction residuals by applying phase retrieval to all segments ($L=80$) of the cell sample captured from one camera. With our method, the residual reduces by around one-third (after $k/N=200$~iterations) with a much smaller spread, demonstrating a more robust object and pupil co-recovery.\relax }}{5}{figure.caption.5}}
\newlabel{fig:adaptive-step}{{S4}{5}{{\bf Adaptive step size improves pupil function recovery.} (a)~Recovered phase component of pupil function with a constant step size, i.e.\ at $\beta =1$, compared to (b)~at $\beta = 10^{-6}.$ Symbols $(\rho _x, \rho _y)$ are the local coordinates of the pupil function. (c)~Comparison of reconstruction residuals by applying phase retrieval to all segments ($L=80$) of the cell sample captured from one camera. With our method, the residual reduces by around one-third (after $k/N=200$~iterations) with a much smaller spread, demonstrating a more robust object and pupil co-recovery.\relax }{figure.caption.5}{}}
\citation{Nakamura2005}
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\@writefile{lof}{\contentsline {figure}{\numberline {S5}{\ignorespaces {\bf  Improving the dynamic range of fluorescence images with digital averaging.} (b)~Single frame at gain $g_\mathrm  {amp} = 8$; (c)~averaging 10~frames at gain $g_\mathrm  {amp} = 8$; Suppressing the band-like pattern noise for (c)~a single frame, and (d)~the digital average of 10~frames. All images are contrast-stretched to highlight the background noise and artifacts. Scale bar: $20\tmspace  +\thinmuskip {.1667em}\si {\micro \meter }.$\relax }}{6}{figure.caption.6}}
\newlabel{fig:digital-averaging}{{S5}{6}{{\bf Improving the dynamic range of fluorescence images with digital averaging.} (b)~Single frame at gain $g_\mathrm {amp} = 8$; (c)~averaging 10~frames at gain $g_\mathrm {amp} = 8$; Suppressing the band-like pattern noise for (c)~a single frame, and (d)~the digital average of 10~frames. All images are contrast-stretched to highlight the background noise and artifacts. Scale bar: $20\micron .$\relax }{figure.caption.6}{}}
\bibdata{my_references}
\bibcite{Kim2016}{1}
\bibcite{Yeh2015}{2}
\bibcite{Lu2016}{3}
\bibcite{Tian2015}{4}
\bibcite{Pan2017}{5}
\bibcite{Hou2018}{6}
\bibcite{Tian2014}{7}
\bibcite{Ou2014}{8}
\bibcite{Widrow1961}{9}
\bibcite{Schuchman1964}{10}
\bibcite{Vanderkooy1984}{11}
\bibcite{Roberts1962}{12}
\bibcite{Balsam2012}{13}
\bibcite{Nakamura2005}{14}
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\@writefile{toc}{\contentsline {paragraph}{Suppressing the power-line noise}{7}{equation.Alph0.19}}
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\@writefile{toc}{\contentsline {section}{\hspace  *{-\tocsep }References}{7}{figure.caption.10}}
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\@writefile{lof}{\contentsline {figure}{\numberline {S6}{\ignorespaces {\bf  Surface flatness of the polystyrene samples, analyzed by the scientific-grade FPM.}\relax }}{8}{figure.caption.7}}
\newlabel{fig:sample-flatness}{{S6}{8}{{\bf Surface flatness of the polystyrene samples, analyzed by the scientific-grade FPM.}\relax }{figure.caption.7}{}}
\@writefile{lof}{\contentsline {figure}{\numberline {S7}{\ignorespaces {\bf  Computationally refocused phase images at off-axis locations.} (a)~Raw intensity image of the entire field-of-view of the U2OS cell line. Also shown are the FPM Phase reconstruction (b)~halfway from the edge of the field-of-view; and (c)~close to the edge of the field-of-view. \relax }}{9}{figure.caption.8}}
\newlabel{fig:depth-of-focus-offaxis}{{S7}{9}{{\bf Computationally refocused phase images at off-axis locations.} (a)~Raw intensity image of the entire field-of-view of the U2OS cell line. Also shown are the FPM Phase reconstruction (b)~halfway from the edge of the field-of-view; and (c)~close to the edge of the field-of-view. \relax }{figure.caption.8}{}}
\@writefile{lof}{\contentsline {figure}{\numberline {S8}{\ignorespaces {\bf  FPM phase quality can be impacted by the plate material.} Grenier UV-Star plates, originally designed for photo-chemical studies in the ultraviolet excitation wavelengths, has a more pronounced uneven surface than Cell~Star plates. Such a surface introduces (a)~speckle-like background artifacts, thus end up as background interference of (b)~the raw intensity images, and in turn causes background fluctuation of (c)~the reconstructed FPM phase images. In contrast, the background artifacts are negligible for Cell Star plates. The speckle grains have a similar size range to that of biological cells, and coincide the same focal plane, so cannot be suppressed effectively by FPM. Scalebar $=100\tmspace  +\thinmuskip {.1667em}\si {\micro \meter }.$\relax }}{10}{figure.caption.9}}
\newlabel{fig:background-speckle}{{S8}{10}{{\bf FPM phase quality can be impacted by the plate material.} Grenier UV-Star plates, originally designed for photo-chemical studies in the ultraviolet excitation wavelengths, has a more pronounced uneven surface than Cell~Star plates. Such a surface introduces (a)~speckle-like background artifacts, thus end up as background interference of (b)~the raw intensity images, and in turn causes background fluctuation of (c)~the reconstructed FPM phase images. In contrast, the background artifacts are negligible for Cell Star plates. The speckle grains have a similar size range to that of biological cells, and coincide the same focal plane, so cannot be suppressed effectively by FPM. Scalebar $=100\micron .$\relax }{figure.caption.9}{}}
\@writefile{lof}{\contentsline {figure}{\numberline {S9}{\ignorespaces {\bf  Spectra of laser, fluorophore (eGFP) and filter set for fluorescence microscopy.} The multimode diode laser (Nichia NUBM07) is filtered with a laser clean up filter of a $5\tmspace  +\thinmuskip {.1667em}\si {\nano \meter }$ bandwidth (Semrock FF01-465/5).\relax }}{10}{figure.caption.10}}
\newlabel{fig:emission-spectrum}{{S9}{10}{{\bf Spectra of laser, fluorophore (eGFP) and filter set for fluorescence microscopy.} The multimode diode laser (Nichia NUBM07) is filtered with a laser clean up filter of a $5\,\si {\nano \meter }$ bandwidth (Semrock FF01-465/5).\relax }{figure.caption.10}{}}
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