@article {69880,
	title = {DeepPD: Joint phase and object estimation from phase diversity with neural calibration of a deformable mirror},
	journal = {arXiv},
	year = {2025},
	month = {2025 Apr 19},
	abstract = {<h4>Sample-induced aberrations and optical imperfections limit the resolution of fluorescence microscopy. Phase diversity is a powerful technique that leverages complementary phase information in sequentially acquired images with deliberately introduced aberrations--the phase diversities--to enable phase and object reconstruction and restore diffraction-limited resolution. These phase diversities are typically introduced into the optical path via a deformable mirror. Existing phase-diversity-based methods are limited to Zernike modes, require large numbers of diversity images, or depend on accurate mirror calibration--which are all suboptimal. We present DeepPD, a deep learning-based framework that combines neural representations of the object and wavefront with a learned model of the deformable mirror to jointly estimate both object and phase from only five images. DeepPD improves robustness and reconstruction quality over previous approaches, even under severe aberrations. We demonstrate its performance on calibration targets and biological samples, including immunolabeled myosin in fixed PtK2 cells.</h4>
},
	doi = {10.48550/arxiv.2504.14157},
	url = {https://doi.org/10.48550/arxiv.2504.14157},
	author = {Magdalena C. Schneider and Courtney Johnson and C{\'e}dric Allier and Larissa Heinrich and Diane Adjavon and Joren Husic and Patrick La Riviere and Stephan Saalfeld and Hari Shroff}
}
@article {68193,
	title = {Architecture and dynamics of a novel desmosome-endoplasmic reticulum organelle},
	journal = {bioRxiv},
	year = {2022},
	month = {2022 Jul 08},
	abstract = {<p>The endoplasmic reticulum (ER) forms a dynamic network that contacts other cellular membranes to regulate stress responses, calcium signaling, and lipid transfer. Using high-resolution volume electron microscopy, we find that the ER forms a previously unknown association with keratin intermediate filaments and desmosomal cell-cell junctions. Peripheral ER assembles into mirror image-like arrangements at desmosomes and exhibits nanometer proximity to keratin filaments and the desmosome cytoplasmic plaque. ER tubules exhibit stable associations with desmosomes, and perturbation of desmosomes or keratin filaments alters ER organization and mobility. These findings indicate that desmosomes and the keratin cytoskeleton pattern the distribution of the ER network. Overall, this study reveals a previously unknown subcellular architecture defined by the structural integration of ER tubules with an epithelial intercellular junction.</p>
},
	doi = {10.1101/2022.07.07.499185},
	url = {https://doi.org/10.1101/2022.07.07.499185},
	author = {Navaneetha Krishnan Bharathan and William Giang and Jesse S. Aaron and Satya Khuon and Teng-Leong Chew and Stephan Preibisch and Eric T. Trautman and Larissa Heinrich and John Bogovic and Davis Bennett and David Ackerman and Woohyun Park and Alyson Petruncio and Aubrey V. Weigel and Stephan Saalfeld and COSEM Project Team and A. Wayne Vogl and Sara N. Stahley and Andrew P. Kowalczyk}
}
