Article
Multidisciplinary Sciences
Morteza J. Siavashani, Iman Naghedi, Vahid Abbasian, Ehsan A. Akhlaghi, Mohammad A. Charsooghi, Mohammad Taghi Tavassoly, Ali-Reza Moradi
Summary: The study introduces a new method for quantitative phase imaging of cells using scanning diffractometry, which is non-contact and vibration-immune, for acquiring 3D cell images. Through Fresnel diffractometry, precise measurements of cell displacement can be achieved and applied to imaging different cell types.
SCIENTIFIC REPORTS
(2021)
Article
Biochemical Research Methods
Simao Coelho, Jongho Baek, James Walsh, J. Justin Gooding, Katharina Gaus
Summary: This method describes how to implement mechanical motion correction in super-resolution imaging, including drift control, focus locking and adjustment, and rapid repositioning. The approach has been proven to reduce drift, improve imaging quality, and is suitable for single-molecule and super-resolution imaging.
Article
Optics
Junjing Deng, Yudong Yao, Yi Jiang, Si Chen, Tim M. Mooney, Jeffrey A. Klug, Fabricio S. Marin, Christian Roehrig, Ke Yue, Curt Preissner, Zhonghou Cai, Barry Lai, Stefan Vogt
Summary: Ptychography is a high-resolution diffraction imaging technique that is sensitive to experimental variations. High-speed data acquisition with short exposure can minimize the impact of experimental variations, and continuous multi-pass scan via high-speed ptychography can achieve high-resolution imaging. This low-dose scan strategy is important for radiation-sensitive sample studies and time-resolved imaging.
Article
Multidisciplinary Sciences
Grigorii Timin, Michel C. Milinkovitch
Summary: Imaging collagen network architecture is crucial for understanding tissue mechanical properties in developmental and cancer biology. This study presents a simple and robust method using 'Fast Green' dye for whole-mount collagen staining, enabling exceptional visualization of collagen 3D network via confocal or light-sheet microscopy, compatible with solvent-based tissue clearing and immunostaining.
Review
Optics
Sophie Brasselet, Miguel A. Alonso
Summary: This review aims to provide a summary of concepts and techniques behind orientation and structural imaging at the molecular level, from ensemble microscopy in 2D to single-molecule super-resolution microscopy in 3D.
Article
Optics
Jiajia Chen, Zhenhong Du, Chenhao Xu, Xiao Xiao, Wei Gong, Ke Si
Summary: Here we report an ultrafast 3D histological imaging scheme based on optimized selective plane illumination microscopy (mSPIM), a minutes-time scale clearing method (FOCM), and a deep learning-based image enhancement algorithm (SRACNet) to realize histological preparation and imaging of clinical tissues. Our scheme enables fast imaging at micron-level resolution and demonstrates detailed 3D morphological connections that are difficult to identify in conventional 2D histology.
Article
Optics
Bo Xiong, Tianyi Zhu, Yuhan Xiang, Xiaopeng Li, Jinqiang Yu, Zheng Jiang, Yihan Niu, Dong Jiang, Xu Zhang, Lu Fang, Jiamin Wu, Qionghai Dai
Summary: MiSLFM utilizes a tilted mirror to achieve super-resolved axial resolution with a single objective, expanding the depth of field of LFM. It allows observation of various organelle interactions and intercellular interactions, as well as more robust blood cell tracking in zebrafish larvae under low light conditions.
LIGHT-SCIENCE & APPLICATIONS
(2021)
Article
Biochemical Research Methods
Yu-Jui Fan, Han-Yun Hsieh, Sheng-Fang Tsai, Cheng-Hsuan Wu, Chia-Ming Lee, Yen-Ting Liu, Chieh-Han Lu, Shu-Wei Chang, Bi-Chang Chen
Summary: The study developed a continuous cell-imaging system with subcellular resolution by integrating a microfluidic platform with lattice lightsheet microscopy (LLSM). By using a microfluidic channel sealed with a water refractive index-matched thin film, aberrations of the lightsheet entering the device were reduced, leading to clearer cell images.
Article
Biochemical Research Methods
Xu Mei, Qiyin Fang, P. ravi Selvaganapathy
Summary: Measurement of oxygen concentration in 3D hydrogels is crucial for 3D cell culture and tissue engineering. This study presents a fast and low-cost phosphorescence lifetime imaging design that can accurately measure oxygen concentration in 3D. By combining light-sheet illumination and frequency-domain lifetime measurement, along with a commercial camera, this design is customizable and cost-effective for specific research needs.
BIOMEDICAL OPTICS EXPRESS
(2023)
Review
Chemistry, Physical
Oleksii Nevskyi, Dominik Woell
Summary: This review discusses the application of super-resolution fluorescence microscopy techniques in nano- and microparticles hydrogels, known as nano- or microgels. It summarizes the progress in studying the morphology, internal structure, dynamics, and diffusion of microgels. The ability to super-resolve structures in three dimensions has greatly advanced the research field and allowed impressive 3D imaging of deformed microgels.
ANNUAL REVIEW OF PHYSICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Jeonghwan Son, Biagio Mandracchia, Aaron D. Silva Trenkle, Gabriel A. Kwong, Shu Jia
Summary: PLSOM is a portable 3D fluorescence cytometric imaging technique that offers high resolution, high throughput, and compatibility with commonly adopted microfluidic chips. It can be widely used for 3D flow cytometric investigations.
Article
Physics, Multidisciplinary
Sjoerd Stallinga, Niels Radmacher, Antoine Delon, Joerg Enderlein
Summary: This article discusses the resolution limit of classical optical microscopy and explores the optimal optical transfer function (OTF) for producing the sharpest images. The findings have important applications in developing deconvolution algorithms for microscopy images and guiding the design of optical systems to achieve optimal imaging. The results can also be generalized to nonoptical imaging fields, such as telescopic imaging, ultrasound imaging, and magnetic resonance imaging.
PHYSICAL REVIEW RESEARCH
(2022)
Article
Optics
Mary Grace M. Velasco, Mengyang Zhang, Jacopo Antonello, Peng Yuan, Edward S. Allgeyer, Dennis May, Ons M'Saad, Phylicia Kidd, Andrew E. S. Barentine, Valentina Greco, Jaime Grutzendler, Martin J. Booth, Joerg Bewersdorf
Summary: STED microscopy allows for three-dimensional visualization of dynamic nanoscale structures in living cells, but imaging deep inside biological tissue faces challenges. Researchers have developed a STED system that overcomes these challenges by combining various technologies to achieve deep aberration-corrected three-dimensional super-resolution imaging.
Article
Multidisciplinary Sciences
F. K. Janiak, P. Bartel, M. R. Bale, T. Yoshimatsu, E. Komulainen, M. Zhou, K. Staras, L. L. Prieto-Godino, T. Euler, M. Maravall, T. Baden
Summary: This study presents a low-cost, easily implemented and flexible design for two-photon microscopy, expanding the 3D field of view and allowing the bending of imaging planes to follow natural curvatures in biological structures.
NATURE COMMUNICATIONS
(2022)
Article
Nanoscience & Nanotechnology
Yifeng Xiang, Junxue Chen, Xi Tang, Ruxue Wang, Qiwen Zhan, Joseph R. Lakowicz, Douguo Zhang
Summary: Placing an ultrathin silver nanowire with a diameter less than 100 nm on a photonic band gap structure can excite surface plasmons that propagate along two side-walls, leading to the observation of two bright lines. Simulations suggest that the unique phase distribution of plasmons on the two side-walls of the silver nanowire is responsible for the bright lines observed in the far-field. The configuration reported in this work, combined with the sensing ability of surface plasmons to its environment, can function as a sensing platform to monitor environmental changes in the near-field region of the ultrathin nanowire.
Article
Computer Science, Information Systems
Zuzana Ferkova, Petra Urbanova, Dominik Cerny, Marek Zuzi, Petr Matula
MULTIMEDIA TOOLS AND APPLICATIONS
(2020)
Correction
Multidisciplinary Sciences
Lena Maier-Hein, Matthias Eisenmann, Annika Reinke, Sinan Onogur, Marko Stankovic, Patrick Scholz, Tal Arbel, Hrvoje Bogunovic, Andrew P. Bradley, Aaron Carass, Carolin Feldmann, Alejandro F. Frangi, Peter M. Full, Bram van Ginneken, Allan Hanbury, Katrin Honauer, Michal Kozubek, Bennett A. Landman, Keno Maerz, Oskar Maier, Klaus Maier-Hein, Bjoern H. Menze, Henning Mueller, Peter F. Neher, Wiro Niessen, Nasir Rajpoot, Gregory C. Sharp, Korsuk Sirinukunwattana, Stefanie Speidel, Christian Stock, Danail Stoyanov, Abdel Aziz Taha, Fons van der Sommen, Ching-Wei Wang, Marc-Andre Weber, Guoyan Zheng, Pierre Jannin, Annette Kopp-Schneider
NATURE COMMUNICATIONS
(2019)
Article
Biochemical Research Methods
David Wiesner, David Svoboda, Martin Maska, Michal Kozubek
Article
Chemistry, Analytical
Marketa Machalkova, Barbora Pavlatovska, Jan Michalek, Adam Pruska, Karel Stepka, Tereza Necasova, Katarzrna Anna Radaszkiewicz, Michal Kozubek, Jan Smarda, Jan Preisler, Jarmila Navratilova
ANALYTICAL CHEMISTRY
(2019)
Article
Multidisciplinary Sciences
Estibaliz Gomez-de-Mariscal, Martin Maska, Anna Kotrbova, Vendula Pospichalova, Pavel Matula, Arrate Munoz-Barrutia
SCIENTIFIC REPORTS
(2019)
Editorial Material
Biochemical Research Methods
Michal Kozubek
Article
Computer Science, Artificial Intelligence
Lena Maier-Hein, Annika Reinke, Michal Kozubek, Anne L. Martel, Tal Arbel, Matthias Eisenmann, Allan Hanbury, Pierre Jannin, Henning Mueller, Sinan Onogur, Julio Saez-Rodriguez, Bram van Ginneken, Annette Kopp-Schneider, Bennett A. Landman
MEDICAL IMAGE ANALYSIS
(2020)
Article
Oncology
Barbora Pavlatovska, Marketa Machalkova, Petra Brisudova, Adam Pruska, Karel Stepka, Jan Michalek, Tereza Necasova, Petr Benes, Jan Smarda, Jan Preisler, Michal Kozubek, Jarmila Navratilova
FRONTIERS IN ONCOLOGY
(2020)
Correction
Multidisciplinary Sciences
Sarthak Pati, Ujjwal Baid, Brandon Edwards, Micah Sheller, Shih-Han Wang, G. Anthony Reina, Patrick Foley, Alexey Gruzdev, Deepthi Karkada, Christos Davatzikos, Chiharu Sako, Satyam Ghodasara, Michel Bilello, Suyash Mohan, Philipp Vollmuth, Gianluca Brugnara, Chandrakanth J. Preetha, Felix Sahm, Klaus Maier-Hein, Maximilian Zenk, Martin Bendszus, Wolfgang Wick, Evan Calabrese, Jeffrey Rudie, Javier Villanueva-Meyer, Soonmee Cha, Madhura Ingalhalikar, Manali Jadhav, Umang Pandey, Jitender Saini, John Garrett, Matthew Larson, Robert Jeraj, Stuart Currie, Russell Frood, Kavi Fatania, Raymond Y. Huang, Ken Chang, Carmen Balana, Jaume Capellades, Josep Puig, Johannes Trenkler, Josef Pichler, Georg Necker, Andreas Haunschmidt, Stephan Meckel, Gaurav Shukla, Spencer Liem, Gregory S. Alexander, Joseph Lombardo, Joshua D. Palmer, Adam E. Flanders, Adam P. Dicker, Haris I. Sair, Craig K. Jones, Archana Venkataraman, Meirui Jiang, Tiffany Y. So, Cheng Chen, Pheng Ann Heng, Qi Dou, Michal Kozubek, Filip Lux, Jan Michalek, Petr Matula, Milos Kerkovsky, Tereza Koprivova, Marek Dostal, Vaclav Vybihal, Michael A. Vogelbaum, J. Ross Mitchell, Joaquim Farinhas, Joseph A. Maldjian, Chandan Ganesh Bangalore Yogananda, Marco C. Pinho, Divya Reddy, James Holcomb, Benjamin C. Wagner, Benjamin M. Ellingson, Timothy F. Cloughesy, Catalina Raymond, Talia Oughourlian, Akifumi Hagiwara, Chencai Wang, Minh-Son To, Sargam Bhardwaj, Chee Chong, Marc Agzarian, Alexandre Xavier Falcao, Samuel B. Martins, Bernardo C. A. Teixeira, Flavia Sprenger, David Menotti, Diego R. Lucio, Pamela LaMontagne, Daniel Marcus, Benedikt Wiestler, Florian Kofler, Ivan Ezhov, Marie Metz, Rajan Jain, Matthew Lee, Yvonne W. Lui, Richard McKinley, Johannes Slotboom, Piotr Radojewski, Raphael Meier, Roland Wiest, Derrick Murcia, Eric Fu, Rourke Haas, John Thompson, David Ryan Ormond, Chaitra Badve, Andrew E. Sloan, Vachan Vadmal, Kristin Waite, Rivka R. Colen, Linmin Pei, Murat Ak, Ashok Srinivasan, J. Rajiv Bapuraj, Arvind Rao, Nicholas Wang, Ota Yoshiaki, Toshio Moritani, Sevcan Turk, Joonsang Lee, Snehal Prabhudesai, Fanny Moron, Jacob Mandel, Konstantinos Kamnitsas, Ben Glocker, Luke V. M. Dixon, Matthew Williams, Peter Zampakis, Vasileios Panagiotopoulos, Panagiotis Tsiganos, Sotiris Alexiou, Ilias Haliassos, Evangelia I. Zacharaki, Konstantinos Moustakas, Christina Kalogeropoulou, Dimitrios M. Kardamakis, Yoon Seong Choi, Seung-Koo Lee, Jong Hee Chang, Sung Soo Ahn, Bing Luo, Laila Poisson, Ning Wen, Pallavi Tiwari, Ruchika Verma, Rohan Bareja, Ipsa Yadav, Jonathan Chen, Neeraj Kumar, Marion Smits, Sebastian R. van der Voort, Ahmed Alafandi, Fatih Incekara, Maarten M. J. Wijnenga, Georgios Kapsas, Renske Gahrmann, Joost W. Schouten, Hendrikus J. Dubbink, Arnaud J. P. E. Vincent, Martin J. van den Bent, Pim J. French, Stefan Klein, Yading Yuan, Sonam Sharma, Tzu-Chi Tseng, Saba Adabi, Simone P. Niclou, Olivier Keunen, Ann-Christin Hau, Martin Vallieres, David Fortin, Martin Lepage, Bennett Landman, Karthik Ramadass, Kaiwen Xu, Silky Chotai, Lola B. Chambless, Akshitkumar Mistry, Reid C. Thompson, Yuriy Gusev, Krithika Bhuvaneshwar, Anousheh Sayah, Camelia Bencheqroun, Anas Belouali, Subha Madhavan, Thomas C. Booth, Alysha Chelliah, Marc Modat, Haris Shuaib, Carmen Dragos, Aly Abayazeed, Kenneth Kolodziej, Michael Hill, Ahmed Abbassy, Shady Gamal, Mahmoud Mekhaimar, Mohamed Qayati, Mauricio Reyes, Ji Eun Park, Jihye Yun, Ho Sung Kim, Abhishek Mahajan, Mark Muzi, Sean Benson, Regina G. H. Beets-Tan, Jonas Teuwen, Alejandro Herrera-Trujillo, Maria Trujillo, William Escobar, Ana Abello, Jose Bernal, Jhon Gomez, Joseph Choi, Stephen Baek, Yusung Kim, Heba Ismael, Bryan Allen, John M. Buatti, Aikaterini Kotrotsou, Hongwei Li, Tobias Weiss, Michael Weller, Andrea Bink, Bertrand Pouymayou, Hassan F. Shaykh, Joel Saltz, Prateek Prasanna, Sampurna Shrestha, Kartik M. Mani, David Payne, Tahsin Kurc, Enrique Pelaez, Heydy Franco-Maldonado, Francis Loayza, Sebastian Quevedo, Pamela Guevara, Esteban Torche, Cristobal Mendoza, Franco Vera, Elvis Rios, Eduardo Lopez, Sergio A. Velastin, Godwin Ogbole, Mayowa Soneye, Dotun Oyekunle, Olubunmi Odafe-Oyibotha, Babatunde Osobu, Mustapha Shu'aibu, Adeleye Dorcas, Farouk Dako, Amber L. Simpson, Mohammad Hamghalam, Jacob J. Peoples, Ricky Hu, Anh Tran, Danielle Cutler, Fabio Y. Moraes, Michael A. Boss, James Gimpel, Deepak Kattil Veettil, Kendall Schmidt, Brian Bialecki, Sailaja Marella, Cynthia Price, Lisa Cimino, Charles Apgar, Prashant Shah, Bjoern Menze, Jill S. Barnholtz-Sloan, Jason Martin, Spyridon Bakas
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Sarthak Pati, Ujjwal Baid, Brandon Edwards, Micah Sheller, Shih-Han Wang, G. Anthony Reina, Patrick Foley, Alexey Gruzdev, Deepthi Karkada, Christos Davatzikos, Chiharu Sako, Satyam Ghodasara, Michel Bilello, Suyash Mohan, Philipp Vollmuth, Gianluca Brugnara, Chandrakanth J. Preetha, Felix Sahm, Klaus Maier-Hein, Maximilian Zenk, Martin Bendszus, Wolfgang Wick, Evan Calabrese, Jeffrey Rudie, Javier Villanueva-Meyer, Soonmee Cha, Madhura Ingalhalikar, Manali Jadhav, Umang Pandey, Jitender Saini, John Garrett, Matthew Larson, Robert Jeraj, Stuart Currie, Russell Frood, Kavi Fatania, Raymond Y. Huang, Ken Chang, Carmen Balana, Jaume Capellades, Josep Puig, Johannes Trenkler, Josef Pichler, Georg Necker, Andreas Haunschmidt, Stephan Meckel, Gaurav Shukla, Spencer Liem, Gregory S. Alexander, Joseph Lombardo, Joshua D. Palmer, Adam E. Flanders, Adam P. Dicker, Haris I. Sair, Craig K. Jones, Archana Venkataraman, Meirui Jiang, Tiffany Y. So, Cheng Chen, Pheng Ann Heng, Qi Dou, Michal Kozubek, Filip Lux, Jan Michalek, Petr Matula, Milos Kerkovsky, Tereza Koprivova, Marek Dostal, Vaclav Vybihal, Michael A. Vogelbaum, J. Ross Mitchell, Joaquim Farinhas, Joseph A. Maldjian, Chandan Ganesh Bangalore Yogananda, Marco C. Pinho, Divya Reddy, James Holcomb, Benjamin C. Wagner, Benjamin M. Ellingson, Timothy F. Cloughesy, Catalina Raymond, Talia Oughourlian, Akifumi Hagiwara, Chencai Wang, Minh-Son To, Sargam Bhardwaj, Chee Chong, Marc Agzarian, Alexandre Xavier Falcao, Samuel B. Martins, Bernardo C. A. Teixeira, Flavia Sprenger, David Menotti, Diego R. Lucio, Pamela La Montagne, Daniel Marcus, Benedikt Wiestler, Florian Kofler, Ivan Ezhov, Marie Metz, Rajan Jain, Matthew Lee, Yvonne W. Lui, Richard McKinley, Johannes Slotboom, Piotr Radojewski, Raphael Meier, Roland Wiest, Derrick Murcia, Eric Fu, Rourke Haas, John Thompson, David Ryan Ormond, Chaitra Badve, Andrew E. Sloan, Vachan Vadmal, Kristin Waite, Rivka R. Colen, Linmin Pei, Murat Ak, Ashok Srinivasan, J. Rajiv Bapuraj, Arvind Rao, Nicholas Wang, Ota Yoshiaki, Toshio Moritani, Sevcan Turk, Joonsang Lee, Snehal Prabhudesai, Fanny Moron, Jacob Mandel, Konstantinos Kamnitsas, Glocker Ben, Luke V. M. Dixon, Matthew Williams, Peter Zampakis, Vasileios Panagiotopoulos, Panagiotis Tsiganos, Sotiris Alexiou, Ilias Haliassos, Evangelia I. Zacharaki, Konstantinos Moustakas, Christina Kalogeropoulou, Dimitrios M. Kardamakis, Yoon Seong Choi, Seung-Koo Lee, Jong Hee Chang, Sung Soo Ahn, Bing Luo, Laila Poisson, Ning Wen, Pallavi Tiwari, Ruchika Verma, Rohan Bareja, Ipsa Yadav, Jonathan Chen, Neeraj Kumar, Marion Smits, Sebastian R. van der Voort, Ahmed Alafandi, Fatih Incekara, Maarten M. J. Wijnenga, Georgios Kapsas, Renske Gahrmann, Joost W. Schouten, Hendrikus J. Dubbink, Arnaud J. P. E. Vincent, Martin J. van den Bent, Pim J. French, Stefan Klein, Yading Yuan, Sonam Sharma, Tzu-Chi Tseng, Saba Adabi, Simone P. Niclou, Olivier Keunen, Ann-Christin Hau, Martin Vallieres, David Fortin, Martin Lepage, Bennett Landman, Karthik Ramadass, Kaiwen Xu, Silky Chotai, Lola B. Chambless, Akshitkumar Mistry, Reid C. Thompson, Yuriy Gusev, Krithika Bhuvaneshwar, Anousheh Sayah, Camelia Bencheqroun, Anas Belouali, Subha Madhavan, Thomas C. Booth, Alysha Chelliah, Marc Modat, Haris Shuaib, Carmen Dragos, Aly Abayazeed, Kenneth Kolodziej, Michael Hill, Ahmed Abbassy, Shady Gamal, Mahmoud Mekhaimar, Mohamed Qayati, Mauricio Reyes, Ji Eun Park, Jihye Yun, Ho Sung Kim, Abhishek Mahajan, Mark Muzi, Sean Benson, Regina G. H. Beets-Tan, Jonas Teuwen, Alejandro Herrera-Trujillo, Maria Trujillo, William Escobar, Ana Abello, Jose Bernal, Jhon Gomez, Joseph Choi, Stephen Baek, Yusung Kim, Heba Ismael, Bryan Allen, John M. Buatti, Aikaterini Kotrotsou, Hongwei Li, Tobias Weiss, Michael Weller, Andrea Bink, Bertrand Pouymayou, Hassan F. Shaykh, Joel Saltz, Prateek Prasanna, Sampurna Shrestha, Kartik M. Mani, David Payne, Tahsin Kurc, Enrique Pelaez, Heydy Franco-Maldonado, Francis Loayza, Sebastian Quevedo, Pamela Guevara, Esteban Torche, Cristobal Mendoza, Franco Vera, Elvis Rios, Eduardo Lopez, Sergio A. Velastin, Godwin Ogbole, Mayowa Soneye, Dotun Oyekunle, Olubunmi Odafe-Oyibotha, Babatunde Osobu, Mustapha Shu'aibu, Adeleye Dorcas, Farouk Dako, Amber L. Simpson, Mohammad Hamghalam, Jacob J. Peoples, Ricky Hu, Anh Tran, Danielle Cutler, Fabio Y. Moraes, Michael A. Boss, James Gimpel, Deepak Kattil Veettil, Kendall Schmidt, Brian Bialecki, Sailaja Marella, Cynthia Price, Lisa Cimino, Charles Apgar, Prashant Shah, Bjoern Menze, Jill S. Barnholtz-Sloan, Jason Martin, Spyridon Bakas
Summary: This study presents the largest federated learning (FL) research to-date, involving data from 71 sites across 6 continents. By only sharing numerical model updates, the study successfully generates an automatic tumor boundary detector for glioblastoma and demonstrates significant improvements in tumor delineation.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Martin Maska, Vladimir Ulman, Pablo Delgado-Rodriguez, Estibaliz Gomez-de-Mariscal, Tereza Necasova, Fidel A. Guerrero Pena, Tsang Ing Ren, Elliot M. Meyerowitz, Tim Scherr, Katharina Loeffler, Ralf Mikut, Tianqi Guo, Yin Wang, Jan P. Allebach, Rina Bao, Noor M. Al-Shakarji, Gani Rahmon, Imad Eddine Toubal, Kannappan Palaniappan, Filip Lux, Petr Matula, Ko Sugawara, Klas E. G. Magnusson, Layton Aho, Andrew R. Cohen, Assaf Arbelle, Tal Ben-Haim, Tammy Riklin Raviv, Fabian Isensee, Paul F. Jaeger, Klaus H. Maier-Hein, Yanming Zhu, Cristina Ederra, Ainhoa Urbiola, Erik Meijering, Alexandre Cunha, Arrate Munoz-Barrutia, Michal Kozubek, Carlos Ortiz-de-Solorzano
Summary: The Cell Tracking Challenge is a benchmarking initiative that has made significant improvements since 2017, including the creation of a new segmentation-only benchmark and the addition of diverse and complex datasets to the repository. A silver standard reference corpus has been created based on competitive results, which will benefit data-hungry deep learning-based strategies. This updated analysis provides practical conclusions for developers and users of cell segmentation and tracking algorithms, highlighting the advancements in both 2D and 3D algorithms.
Article
Computer Science, Artificial Intelligence
Sophie Ostmeier, Brian Axelrod, Fabian Isensee, Jeroen Bertels, Michael Mlynash, Soren Christensen, Maarten G. Lansberg, Gregory W. Albers, Rajen Sheth, Benjamin F. J. Verhaaren, Abdelkader Mahammedi, Li-Jia Li, Greg Zaharchuk, Jeremy J. Heit
Summary: Performance metrics for medical image segmentation models are crucial in evaluating the agreement between predicted segmentation and reference annotation. However, commonly used metrics fail to capture the impact of mismatch between clinical practice and public dataset settings, particularly when dealing with challenging segmentation tasks, low signal pathologies, and uncertain, small, or empty reference annotations. Rethinking the evaluation methods is necessary to effectively assess the clinical value of such models.
MEDICAL IMAGE ANALYSIS
(2023)
Proceedings Paper
Engineering, Biomedical
Aleksandra Melnikova, Petr Matula
Summary: The algorithm aims to fuse simply connected segmentation masks of complex and variable shapes commonly seen in cell imaging. It works through three main phases: detecting geodesic ends, optimal matching of ends, and contour averaging. Compared to commonly used pixel-wise fusion algorithms and geometric median shapes, the algorithm outperforms in visual quality and better representation of protrusions.
2021 IEEE 18TH INTERNATIONAL SYMPOSIUM ON BIOMEDICAL IMAGING (ISBI)
(2021)
Proceedings Paper
Engineering, Biomedical
Gem Emre Akbas, Michal Kozubek
2020 IEEE 17TH INTERNATIONAL SYMPOSIUM ON BIOMEDICAL IMAGING (ISBI 2020)
(2020)
Article
Cell Biology
Anna Kotrbova, Karel Stepka, Martin Maska, Jakub Jozef Palenik, Ladislav Ilkovics, Dobromila Klemova, Marek Kravec, Frantisek Hubatka, Zankruti Dave, Ales Hampl, Vitezslav Bryja, Pavel Matula, Vendula Pospichalova
JOURNAL OF EXTRACELLULAR VESICLES
(2019)