Microscopy preLights

Posted by FocalPlane, on 23 September 2021

Here is your monthly post with a curated list of interesting microscopy-related preprints as well as preprint highlights written by preLighters. Thank you to the preLights community and the Node community manager, Helen Zenner, who helped us create this list.

Here is a curated selection of preprints and highlights published in the last month:

Imaging Tools

Live imaging YAP signaling in vivo with fusion reporter mice. Bin Gu, Brian Bradshaw, Min Zhu, Yu Sun, Sevan Hopyan, Janet Rossant

Python-Microscope: A new open source Python library for the control of microscopes. David Miguel Susano Pinto, Mick A Phillips, Nicholas Hall, Julio Mateos–Langerak, Danail Stoychev, Tiago Susano Pinto, Martin J Booth, Ilan Davis, Ian M Dobbie

Fast 3D Clear: A Fast, Aqueous, Reversible Three-Day Tissue Clearing Method for Adult and Embryonic Mouse Brain and Whole Body. Stylianos Kosmidis, Adrian Negrean, Alex Dranovsky, Attila Losonczy, Eric R. Kandel

Figure panels extracted from Kosmidis *et al.*

tdLanYFP, a yellow, bright, photostable and pH insensitive fluorescent protein for live cell imaging and FRET-based sensing strategies. Yasmina Bousmah, Hana Valenta, Giulia Bertolin, Utkarsh Singh, Valérie Nicolas, Hélène Pasquier, Marc Tramier, Fabienne Merola, Marie Erard

Figure panels extracted from Bousmah *et al.*

Microscopy in cell biology, neuroscience, development and other fields

Symmetry breaking of hPSCs in micropattern generates a polarized spinal cord-like organoid (pSCO) with dorsoventral organization. Kyubin Seo, Subin Cho, Ju-Hyun Lee, June Hoan Kim, Boram Lee, Hwanseok Jang, Youngju Kim, Hyo Min Cho, Sanghyuk Lee, Yongdoo Park, Hee Youn Kim, Taeseob Lee, Woong-Yang Park, Yong Jun Kim, Esther Yang, Dongho Geum, Hyun Kim, Jae Ryun Ryu, Woong Sun

A condensate dynamic instability orchestrates oocyte actomyosin cortex activation. Victoria Tianjing Yan, Arjun Narayanan, Frank Jülicher, Stephan W. Grill

Figure panels extracted from Yan *et al.*

Nanoscale organization of the endogenous ASC speck. Ivo M. Glück, Grusha Primal Mathias, Sebastian Strauss, Thomas S. Ebert, Che Stafford, Ganesh Agam, Suliana Manley, Veit Hornung, Ralf Jungmann, Christian Sieben, Don C. Lamb

Figure panels extracted from Glück *et al.*

Three-dimensional Super-resolved Imaging of Paraffin-embedded Kidney Samples. David Unnersjö-Jess, Amer Ramdedovic, Martin Höhne, Linus Butt, Felix C. Koehler, Roman-Ulrich Müller, Peter F. Hoyer, Hans Blom, Bernhard Schermer, Thomas Benzing

Figure panels extracted from Unnersjö-Jess *et al.*

Microtubule deacetylation reduces cell stiffness to allow the onset of collective cell migration in vivo. CL Marchant, AN Malmi-Kakkada, JA Espina, EH Barriga

Spatiotemporal dynamics of human microglia are linked with brain developmental processes across the lifespan. D.A. Menassa, T.A.O. Muntslag, M. Martin-Estebané, L. Barry-Carroll, M.A. Chapman, I. Adorjan, T. Tyler, B. Turnbull, M.J.J. Rose-Zerilli, J.A.R. Nicoll, Z. Krsnik, I. Kostovic, D. Gomez-Nicola

Visualising the cytoskeletal machinery in neuronal growth cones using cryo-electron tomography. Joseph Atherton, Melissa Stouffer, Fiona Francis, Carolyn A. Moores

Figure panels extracted from Atherton *et al.*

Bioimage analysis

Deep learning-based algorithm for predicting the live birth potential of mouse embryos. Yuta Tokuoka, Takahiro G. Yamada, Daisuke Mashiko, Zenki Ikeda, Tetsuya J. Kobayashi, Kazuo Yamagata, Akira Funahashi

Vesalius: Tissue anatomy from spatial transcriptomic data. Patrick C.N. Martin, Cecilia Lövkvist, Byung-Woo Hong, Kyoung Jae Won

Designing and interpreting 4D tumour spheroid experiments. Ryan J. Murphy, Alexander P. Browning, Gency Gunasingh, Nikolas K. Haass, Matthew J. Simpson

Deep learning-enhanced morphological profiling predicts cell fate dynamics in real-time in hPSCs. Edward Ren, Sungmin Kim, Saad Mohamad, Samuel F. Huguet, Yulin Shi, Andrew R. Cohen, Eugenia Piddini, Rafael Carazo Salas

Evaluation of STED Super-Resolution image quality by image correlation spectroscopy (QuICS). Elena Cerutti, Morgana D’Amico, Isotta Cainero, Gaetano Ivan Dellino Mario Faretta, Giuseppe Vicidomini, Pier Giuseppe Pelicci, Paolo Bianchini, Alberto Diaspro, Luca Lanzanò

CellProfiler Analyst 3.0: Accessible data exploration and machine learning for image analysis. David R. Stirling, Anne E. Carpenter, Beth A. Cimini

preLights

Highlight by Kristina Kuhbandner: Ageing-associated myelin dysfunction drives amyloid deposition in mouse models of Alzheimer’s disease. Constanze Depp, Ting Sun, Andrew Octavian Sasmita, Lena Spieth, Stefan A. Berghoff, Agnes A. Steixner-Kumar, Swati Subramanian, Wiebke Möbius, Sandra Göbbels, Gesine Saher, Silvia Zampar, Oliver Wirths, Maik Thalmann, Takashi Saito, Takaomi Saido, Dilja Krueger-Burg, Riki Kawaguchi, Michael Willem, Christian Haass, Daniel Geschwind, Hannelore Ehrenreich, Ruth Stassart, Klaus-Armin Nave

Figure panels extracted from Depp *et al.*

Highlight by SCELSE Summer School: Cellular chaining influences biofilm formation and structure in Group A Streptococcus. Artur Matysik, Foo Kiong Ho, Alicia Qian Ler Tan, Anuradha Vajjala, Kimberly A. Kline

Figure panels extracted from Matysik *et al.*

Highlight by Srivatsava Viswanadha: Self-organized morphogenesis of a human neural tube in vitro by geometric constraints. Eyal Karzbrun, Aimal H. Khankhel, Heitor C. Megale, Stella M. K. Glasauer, Yofiel Wyle, George Britton, Aryeh Warmflash, Kenneth S. Kosik, Eric D. Siggia, Boris I. Shraiman, Sebastian J. Streichan

Figure panels extracted from Karzbrun *et al.*

Highlight by Julia Grzymkowski: Extracellular mechanical forces drive endocardial cell volume decrease during cardiac valve morphogenesis. Hélène Vignes, Christina Vagena-Pantoula, Mangal Prakash, Caren Norden, Florian Jug, Julien Vermot

Figure panels extracted from Vignes *et al.*

Highlight by Osvaldo Contreras: Multiscale light-sheet organoid imaging framework. Gustavo de Medeiros, Raphael Ortiz, Petr Strnad, Andrea Boni, Francisca Maurer, Prisca Liberali