Article
Biochemistry & Molecular Biology
Palak Dave, Dmitry Goldgof, Lawrence O. Hall, Yaroslav Kolinko, Kurtis Allen, Saeed Alahmari, Peter R. Mouton
Summary: This paper demonstrates the automatic estimation of total cell number in tissue sections through a combination of deep learning and the disector-based optical fractionator method. This method improves accuracy and efficiency by automatically counting cells using unbiased stereology methods, addressing the limitations of conventional stereology techniques, and provides practical applications.
JOURNAL OF CHEMICAL NEUROANATOMY
(2022)
Article
Biochemistry & Molecular Biology
Kevin Adi Kurnia, Bonifasius Putera Sampurna, Gilbert Audira, Stevhen Juniardi, Ross D. Vasquez, Marri Jmelou M. Roldan, Che-Chia Tsao, Chung-Der Hsiao
Summary: Previous methods for measuring protozoan numbers have limitations, but this study establishes an ImageJ-based workflow for high-throughput quantification of ciliate numbers. Among five different methods tested, the deep-learning-based StarDist method displayed the best performance for Tetrahymena cell counting.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Audiology & Speech-Language Pathology
Cathy Yea Won Sung, Melanie Barzik, Tucker Costain, Lizhen Wang, Lisa L. Cunningham
Summary: The mouse utricle model system is the most reliable in vitro preparation for studying mature mammalian hair cells. However, quantifying hair cells efficiently and accurately has been a challenge. This study introduces a semi-automated method that combines immune reactivity for the specific transcription factor Pou4f3 with labeling of activated caspase 3/7 to detect surviving and apoptotic hair cells, enabling faster and more accurate quantification.
Article
Chemistry, Analytical
Robert D. Fennell, Mazhar Sher, Waseem Asghar
Summary: The development of a point-of-care, cost-effective, and easy-to-use assay for the accurate counting of CD4(+) T cells has been achieved, providing a rapid and efficient method for quantifying CD4(+) T cell count.
Article
Computer Science, Interdisciplinary Applications
David Lacalle, Hector Alfonso Castro-Abril, Teodora Randelovic, Cesar Dominguez, Jonathan Heras, Eloy Mata, Gadea Mata, Yolanda Mendez, Vico Pascual, Ignacio Ochoa
Summary: The study developed a generic tool for spheroid segmentation and constructed deep learning models that can be applied to multiple scenarios. This work enables more reliable and comparable analysis of spheroids acquired under different conditions, advancing the understanding of tumor behavior.
COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE
(2021)
Article
Biology
Rebekah Keating Godfrey, Mira Swartzlander, Wulfila Y. Gronenberg
Summary: This study estimated total brain cell numbers for 32 species of Hymenoptera using the isotropic fractionator method, revealing ants have particularly small brains compared to bees and wasps. Small Hymenoptera tend to have proportionally larger brains and higher brain cell densities, similar to trends in most vertebrates. The study establishes the isotropic fractionator as a useful method for comparative studies of brain size evolution in insects.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Kevin Adi Kurnia, Fiorency Santoso, Bonifasius Putera Sampurna, Gilbert Audira, Jong-Chin Huang, Kelvin H-C Chen, Chung-Der Hsiao
Summary: The TCMacro method developed in this study provides a simple and robust way to measure relative tail coiling activities in zebrafish embryos in a high throughput manner. The method is based on dynamic pixel intensity changes in a region of interest, allowing for accurate and batch measurements of tail coiling counts, durations and intervals. The method was successfully validated through neurotoxicity analysis of Tricaine and caffeine, showing dose-dependent decrease and increase in tail coiling activity, respectively.
Article
Multidisciplinary Sciences
Melissa Berni, Stefano Pongolini, Martina Tambassi
Summary: This article introduces an automated image analysis method for studying the behavior of Salmonella in the intestine. By using ImageJ software and the pCHAR-Duo fluorescence reporter plasmid, the intracellular replication of Salmonella can be assessed quickly and accurately. This method is suitable for high-throughput screening experiments and detailed investigation of Salmonella-enterocyte interaction.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2022)
Article
Cell & Tissue Engineering
Takuya Hirose, Jun'ichi Kotoku, Fujio Toki, Emi K. Nishimura, Daisuke Nanba
Summary: DeepACT is a deep learning-based automated cell tracking technology for quality control and identification of cultured human stem cells. It can analyze cell motion and spatial information to evaluate keratinocyte dynamics accurately.
Article
Multidisciplinary Sciences
Alvaro Gomariz, Tiziano Portenier, Cesar Nombela-Arrieta, Orcun Goksel
Summary: The investigation of biological systems with three-dimensional microscopy requires automatic cell identification methods that accurately predict uncertain outcomes. We propose a framework that integrates deep Bayesian learning and probabilistic spatial analysis to operate on large microscopy images and output probabilistic predictions, revealing spatial patterns in bone marrow datasets.
Article
Biotechnology & Applied Microbiology
Zhiyao Ma, Marcelo Augusto Szymanskide Toledo, Paul Wanek, Mohamed H. Elsafi Mabrouk, Francis Smet, Rock Pulak, Simon Pieske, Tobias Piotrowski, Werner Herfs, Christian Brecher, Robert H. Schmitt, Wolfgang Wagner, Martin Zenke
Summary: This article presents an automated platform for efficient and robust cultivation and differentiation of iPS cells into blood cells. By implementing cell cluster sorting and controlling the size of embryoid bodies (EBs), efficient differentiation of iPS cells can be achieved.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Timo Henneck, Christina Krueger, Andreas Nerlich, Melissa Langer, Leonie Fingerhut, Marta C. Bonilla, Marita Meurer, Sonke von den Berg, Nicole de Buhr, Katja Branitzki-Heinemann, Maren von Koeckritz-Blickwede
Summary: The formation of neutrophil extracellular traps (NETs), a complex structure composed of chromatin fibers and cellular components, was first described in 2004. Quantification of NETs is often done using free DNA, but immuno-fluorescence microscopy with NET-specific markers is necessary for accurate differentiation from necrotic DNA-release. Although manual evaluation is time-consuming and difficult to standardize, it remains widely used due to the lack of standardized methods and limited software tools for NET evaluation. This study compares computer-based methods with manual counting and highlights the limitations and challenges in automated quantification of NETs.
Review
Respiratory System
Matthias Ochs, Julia Schipke
Summary: This primer highlights the use of stereology for quantitative assessment of lung micro-structure and emphasizes its contribution to improving the quality of laboratory work and good scientific practice.
RESPIRATORY RESEARCH
(2021)
Article
Multidisciplinary Sciences
Dou Ye, Suqing Qu, Yinxiang Yang, Zhaoyan Wang, Qian Wang, Weipeng Liu, Fan Zhang, Qian Guan, Xiaohua Wang, Jing Zang, Xin Li, Hengtao Liu, Ruiqin Yao, Zhichun Feng, Zuo Luan
Summary: Immunosuppressants are not suitable for premature infants, but desensitization can induce immune tolerance. In this study, Wistar rat fetuses were injected with hOPCs-1 and returned to the mother. After desensitization, brain and muscle transplantation was performed with hOPCs-1, hNSCs-1, and hOPCs-2. The desensitized group showed higher levels of hOPCs-1 and hNSCs-1 compared to the control group, while hOPCs-2 were rejected. There were significant differences in Treg, CD4CD28, CD8CD28, and CD45RC between the desensitization and control group. Inflammatory cells were lower in the desensitized group with hOPCs-1 and hNSCs-1. hOPCs-1 could differentiate into myelin in the desensitized group. Wistar rats with desensitization developed immune tolerance.
Article
Crystallography
Magnus. J. J. Anderson, Hector. C. C. Basoalto
Summary: This article presents automated stereological methods for approximating the 3D size distribution of unimodal or bimodal precipitate dispersions using 2D and 1D measurements from polydisperse spherical non-penetrating particle dispersions. A method to quantify the uncertainty of the approximation based on the number of sampled particles is introduced and validated with experimental data. Derivation and verification of the analytical stereological expressions are included. Two procedures are presented for estimating the 3D size distribution of bimodal particle populations, depending on the relative size of the populations. These methods are valuable for determining the initial particle size distribution for modeling and characterizing precipitate dispersions.
Article
Neurosciences
Susan J. Tappan, Brian S. Eastwood, Nathan O'Connor, Quanxin Wang, Lydia Ng, David Feng, Bryan M. Hooks, Charles R. Gerfen, Patrick R. Hof, Christoph Schmitz, Jack R. Glaser
JOURNAL OF COMPARATIVE NEUROLOGY
(2019)
Article
Multidisciplinary Sciences
Ruixuan Gao, Shoh M. Asano, Srigokul Upadhyayula, Igor Pisarev, Daniel E. Milkie, Tsung-Li Liu, Ved Singh, Austin Graves, Grace H. Huynh, Yongxin Zhao, John Bogovic, Jennifer Colonell, Carolyn M. Ott, Christopher Zugates, Susan Tappan, Alfredo Rodriguez, Kishore R. Mosaliganti, Shu-Hsien Sheu, H. Amalia Pasolli, Song Pang, C. Shan Xu, Sean G. Megason, Harald Hess, Jennifer Lippincott-Schwartz, Adam Hantman, Gerald M. Rubin, Tom Kirchhausen, Stephan Saalfeld, Yoshinori Aso, Edward S. Boydent, Eric Betzig
Article
Neurosciences
Miguel A. Gama Sosa, Rita De Gasperi, Georgina S. Perez Garcia, Gissel M. Perez, Courtney Searcy, Danielle Vargas, Alicia Spencer, Pierce L. Janssen, Anna E. Tschiffely, Richard M. McCarron, Benjamin Ache, Rajaram Manoharan, William G. Janssen, Susan J. Tappan, Russell W. Hanson, Sam Gandy, Patrick R. Hof, Stephen T. Ahlers, Gregory A. Elder
ACTA NEUROPATHOLOGICA COMMUNICATIONS
(2019)
Article
Multidisciplinary Sciences
Sirisha Achanta, Jonathan Gorky, Clara Leung, Alison Moss, Shaina Robbins, Leonard Eisenman, Jin Chen, Susan Tappan, Maci Heal, Navid Farahani, Todd Huffman, Steve England, Zixi (Jack) Cheng, Rajanikanth Vadigepalli, James S. Schwaber
Article
Physiology
Mahyar Osanlouy, Anita Bandrowski, Bernard de Bono, David Brooks, Antonino M. Cassara, Richard Christie, Nazanin Ebrahimi, Tom Gillespie, Jeffrey S. Grethe, Leonardo A. Guercio, Maci Heal, Mabelle Lin, Niels Kuster, Maryann E. Martone, Esra Neufeld, David P. Nickerson, Elias G. Soltani, Susan Tappan, Joost B. Wagenaar, Katie Zhuang, Peter J. Hunter
Summary: The Data and Resource Center (DRC) of the NIH-funded SPARC program is developing databases, connectivity maps, and simulation tools for the mammalian autonomic nervous system. The experimental data and mathematical models supplied to the DRC by the SPARC consortium are curated, annotated and semantically linked via a single knowledgebase. A data portal has been developed that allows discovery of data and models both via semantic search and via an interface that includes Google Map-like 2D flatmaps for displaying connectivity, and 3D anatomical organ scaffolds that provide a common coordinate framework for cross-species comparisons.
FRONTIERS IN PHYSIOLOGY
(2021)
Article
Multidisciplinary Sciences
Clara Leung, Shaina Robbins, Alison Moss, Maci Heal, Mahyar Osanlouy, Richard Christie, Navid Farahani, Corey Monteith, Jin Chen, Peter Hunter, Susan Tappan, Rajanikanth Vadigepalli, Zixi (Jack) Cheng, James S. Schwaber
Summary: The study developed and analyzed a single-cell scale anatomical map of the rat intrinsic cardiac nervous system (ICNS) across male and female hearts, revealing a reliable structural organization plan and providing a foundation for further analysis in cardiac function and disease. The distribution and clustering of ICNS neurons were highly conserved across all male and female rat hearts with distinct clusters consistently localized, though female hearts had fewer neurons and slightly reduced distribution. The anatomical data from each heart were registered to a geometric scaffold for standardization of common anatomical planes, allowing integration and comparison of multiple experimental results and data types.
Article
Computer Science, Interdisciplinary Applications
A. E. Sullivan, S. J. Tappan, P. J. Angstman, A. Rodriguez, G. C. Thomas, D. M. Hoppes, M. A. Abdul-Karim, M. L. Heal, Jack R. Glaser
Summary: With the advancement in microscopy and computer science, digitally reconstructing, modeling, and quantifying microscopic anatomies has become crucial in various fields of biological research. MBF Bioscience openly documents their Neuromorphological File Specification, which is widely used in the neuroscience community to encourage data reuse and alternative analysis. The format continues to evolve to meet the FAIR data principles and facilitate easy identification and repurposing for downstream applications and investigations.
Article
Neurosciences
Miguel A. Gama Sosa, Rita De Gasperi, Dylan Pryor, Georgina S. Perez Garcia, Gissel M. Perez, Rania Abutarboush, Usmah Kawoos, Seth Hogg, Benjamin Ache, William G. Janssen, Allison Sowa, Timothy Tetreault, David G. Cook, Susan J. Tappan, Sam Gandy, Patrick R. Hof, Stephen T. Ahlers, Gregory A. Elder
Summary: The study found that chronic vascular degenerative changes induced by explosions may affect cerebral blood circulation and neuroinflammation, contributing to the progression of blast-induced post-traumatic outcomes. Specifically, abnormalities in blood vessels and neuronal degeneration may be key targets for potential therapies for blast-induced brain injury.
ACTA NEUROPATHOLOGICA COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Yuanyuan Zhang, Ariege Bizanti, Scott W. Harden, Jin Chen, Kohlton Bendowski, Donald B. Hoover, David Gozal, Kalyanam Shivkumar, Maci Heal, Susan Tappan, Zixi Jack Cheng
Summary: This study provides a detailed neuroanatomical map of the sympathetic innervation of the heart in mice, showing that the sympathetic nerves enter the atria through multiple pathways and have different densities in different regions. The study also finds that sympathetic nerves innervate blood vessels and adipocytes.
SCIENTIFIC REPORTS
(2023)
Article
Neurosciences
Miguel Gama A. Sosa, Rita De Gasperi, Dylan Pryor, Georgina S. Perez S. Garcia, Gissel M. Perez, Rania Abutarboush, Usmah Kawoos, Seth Hogg, Benjamin Ache, Allison Sowa, Timothy Tetreault, Merina Varghese, David G. Cook, Carolyn W. Zhu, Susan J. Tappan, William G. M. Janssen, Patrick R. Hof, Stephen T. Ahlers, Gregory A. Elder
Summary: In the context of modern war theaters, blast exposures in military operations can lead to the development of various mental health disorders associated with post-traumatic stress disorder symptoms. This study focuses on investigating the late neuropathological events associated with cerebrovascular changes induced by repetitive low-level blast-exposures. The findings suggest that the cerebral vasculature is a major target for blast-induced damage, leading to neurovascular degenerative processes.
ACTA NEUROPATHOLOGICA COMMUNICATIONS
(2023)
Article
Neurosciences
Jichao Ma, Duyen Nguyen, Jazune Madas, Ariege Bizanti, Anas Mistareehi, Andrew M. Kwiat, Jin Chen, Mabelle Lin, Richard Christie, Peter Hunter, Maci Heal, Shane Baldwin, Susan Tappan, John B. Furness, Terry L. Powley, Zixi (Jack) Cheng
Summary: By using immunohistochemistry labeling and imaging techniques, the distribution and morphology of CGRP-IR axon innervation in the whole mouse stomach muscular layers were characterized. CGRP-IR axons were found to densely interact with blood vessels and run parallel with the longitudinal and circular muscles, forming contacts with myenteric ganglion neurons. This study provides important information for understanding the role of CGRP-IR axons in gastric function regulation.
JOURNAL OF COMPARATIVE NEUROLOGY
(2023)
Article
Neurosciences
Marina Kovalenko, Austen Milnerwood, James Giordano, Jason St Claire, Jolene R. Guide, Mary Stromberg, Tammy Gillis, Ellen Sapp, Marian DiFiglia, Marcy E. MacDonald, Jeffrey B. Carroll, Jong-Min Lee, Susan Tappan, Lynn Raymond, Vanessa C. Wheeler
JOURNAL OF HUNTINGTONS DISEASE
(2018)
Article
Neurosciences
Susan J. Hendricks, Edwin W. Rubel, Rae Nishi
JOURNAL OF COMPARATIVE NEUROLOGY
(2006)
Article
Neurosciences
SJ Hendricks, PC Brunjes, DL Hill
JOURNAL OF COMPARATIVE NEUROLOGY
(2004)