pypi: scikit-image | Projects | Ecosyste.ms: Papers

10.7717/peerj.6398

Quantitative color profiling of digital images with earth mover’s distance using the R package colordistance
Cited by: 49
Author(s): Hannah Weller, Mark W. Westneat
Software Mentions: 23
Published: almost 6 years ago

10.1186/s12880-021-00551-1

Sensitivity analysis for interpretation of machine learning based segmentation models in cardiac MRI
Cited by: 14
Author(s): Markus J. Ankenbrand, Liliia Shainberg, Michael Hock, David Lohr, Laura M. Schreiber
Software Mentions: 18
Published: almost 4 years ago

10.1186/s40679-016-0031-0

Analyzing microtomography data with Python and the scikit-image library
Cited by: 22
Author(s): Emmanuelle Gouillart, Juan Nunez-Iglesias, Stéfan van der Walt
Software Mentions: 14
Published: almost 8 years ago

10.7554/eLife.55913

An image-based data-driven analysis of cellular architecture in a developing tissue
Cited by: 22
Author(s): Jonas Hartmann, Mie Wong, Elisa Cristina de Proença Rodrigues Gallo, Darren Gilmour
Software Mentions: 14
Published: over 4 years ago

10.1186/s40679-018-0060-y

An open-source software ecosystem for the interactive exploration of ultrafast electron scattering data
Cited by: 11
Author(s): Laurent P. René de Cotret, Martin Otto, Mark J. Stern, Bradley J. Siwick
Software Mentions: 12
Published: about 6 years ago

10.3390/ani11020485

Action Recognition Using a Spatial-Temporal Network for Wild Felines
Cited by: 9
Author(s): Liqi Feng, Yaqin Zhao, Yang Sun, Wenxuan Zhao, Jiaxi Tang
Software Mentions: 12
Published: almost 4 years ago

10.1186/s12859-021-04037-3

InstantDL: an easy-to-use deep learning pipeline for image segmentation and classification
Cited by: 8
Author(s): Dominik J. E. Waibel, Sayedali Shetab Boushehri, Carsten Marr
Software Mentions: 10
Published: over 3 years ago

10.1371/journal.pgen.1008458

Microbial phenotypic heterogeneity in response to a metabolic toxin: Continuous, dynamically shifting distribution of formaldehyde tolerance in Methylobacterium extorquens populations
Cited by: 23
Author(s): Jessica A. Lee, Siavash Riazi, Shahla Nemati, Jannell V. Bazurto, Andreas E. Vasdekis, Benjamin J. Ridenhour, Christopher H. Remien, Christopher J. Marx
Software Mentions: 10
Published: about 5 years ago

10.7717/peerj.453

scikit-image: image processing in Python
Cited by: 3,381
Author(s): Stéfan van der Walt, Johannes L. Schönberger, Juan Nunez-Iglesias, François Boulogne, Joshua D. Warner, Neil Yager, Emmanuelle Gouillart, Tony Yu
Software Mentions: 10
Published: over 10 years ago

10.1016/j.cell.2021.07.017

Whole-body integration of gene expression and single-cell morphology
Cited by: 59
Author(s): Hernando Vergara, Constantin Pape, Kimberly Meechan, Valentyna Zinchenko, Christel Genoud, Adrian Wanner, Kevin Nzumbi Mutemi, Benjamin Titze, Rachel Templin, Paola Bertucci, Oleg Simakov, Wiebke Dürichen, Pedro Machado, Emily L. Savage, Lothar Schermelleh, Yannick Schwab, Rainer W. Friedrich, Anna Kreshuk, Christian Tischer, Detlev Arendt
Software Mentions: 10
Published: about 3 years ago

10.1038/s41598-020-80308-y

A novel retinal ganglion cell quantification tool based on deep learning
Cited by: 22
Author(s): Luca Masin, Marie Claes, Steven Bergmans, Lien Cools, Lien Andries, Benjamin Davis, Lieve Moons, Lies De Groef
Software Mentions: 10
Published: almost 4 years ago

10.1371/journal.pcbi.1008364

pyTFM: A tool for traction force and monolayer stress microscopy
Cited by: 19
Author(s): Andreas Bauer, Magdalena Přechová, Lena Fischer, Ingo Thievessen, Martin Gregor, Ben Fabry
Software Mentions: 9
Published: over 3 years ago

10.3390/cancers13040722

Prognostic and Predictive Value of Integrated Qualitative and Quantitative Magnetic Resonance Imaging Analysis in Glioblastoma
Cited by: 19
Author(s): Maikel Verduin, Sergey Primakov, Inge Compter, Henry C. Woodruff, Sander M. J. van Kuijk, Bram Ramaekers, Maarten te Dorsthorst, Elles G. M. Revenich, Mark ter Laan, Sjoert Pegge, Frederick J. A. Meijer, Jan Beckervordersandforth, Ernst-Jan M. Speel, Benno Küsters, Wendy W.J. de Leng, Monique M. Anten, Martijn P. G. Broen, Linda Ackermans, Olaf Schijns, Onno P.M. Teernstra, Koos E. Hovinga, Marc Vooijs, Vivianne C. G. Tjan‐Heijnen, Daniëlle Eekers, Alida A. Postma, Ann Hoeben
Software Mentions: 9
Published: almost 4 years ago

10.7554/eLife.42448

Respiratory syncytial virus co-opts host mitochondrial function to favour infectious virus production
Cited by: 40
Author(s): Mengjie Hu, Keith E. Schulze, Reena Ghildyal, Darren C. Henstridge, Jacek L. Kolanowski, Elizabeth J. New, Yuning Hong, Alan Hsu, Philip M. Hansbro, Peter Wark, Marie A. Bogoyevitch, David A. Jans
Software Mentions: 8
Published: over 5 years ago

10.3390/plants10050840

Development of an Image Analysis Pipeline to Estimate Sphagnum Colony Density in the Field
Cited by: 1
Author(s): Willem Q. M. van de Koot, Larissa J. J. van Vliet, Wei‐Lun Chen, John Doonan, Cândida Nibau
Software Mentions: 8
Published: over 3 years ago

10.1523/ENEURO.0415-20.2021

Real-Time Closed-Loop Feedback in Behavioral Time Scales Using DeepLabCut
Cited by: 17
Author(s): Keisuke Sehara, Paul Zimmer-Harwood, Matthew E. Larkum, Robert N. S. Sachdev
Software Mentions: 8
Published: almost 4 years ago

10.7717/peerj.2674

jicbioimage: a tool for automated and reproducible bioimage analysis
Cited by: 6
Author(s): Tjelvar S. G. Olsson, Matthew Hartley
Software Mentions: 8
Published: about 8 years ago

10.1371/journal.pcbi.1006269

Evaluating reproducibility of AI algorithms in digital pathology with DAPPER
Cited by: 43
Author(s): Andrea Bizzego, Nicole Bussola, Marco Chierici, Valerio Maggio, Margherita Francescatto, Luca Cima, Marco Cristoforetti, Giuseppe Jurman, Cesare Furlanello
Software Mentions: 7
Published: over 5 years ago

10.1186/s13059-019-1699-y

CellTag Indexing: genetic barcode-based sample multiplexing for single-cell genomics
Cited by: 56
Author(s): Chuner Guo, Wenjun Kong, Kenji Kamimoto, Guillermo C. Rivera-Gonzalez, Xue Yang, Yuhei Kirita, Samantha A. Morris
Software Mentions: 7
Published: over 5 years ago

10.3389/fninf.2017.00044

SamuROI, a Python-Based Software Tool for Visualization and Analysis of Dynamic Time Series Imaging at Multiple Spatial Scales
Cited by: 13
Author(s): Martin Rueckl, Stephen C. Lenzi, Laura Moreno-Velasquez, Daniel Parthier, Dietmar Schmitz, Sten Ruediger, Friedrich W. Johenning
Software Mentions: 7
Published: over 7 years ago

10.7554/eLife.61408

Constructing and optimizing 3D atlases from 2D data with application to the developing mouse brain
Cited by: 13
Author(s): David M. Young, Siavash Fazel Darbandi, Grace B. Schwartz, Zachary Bonzell, Deniz Yuruk, Mai Nojima, Leena Gole, John L.R. Rubenstein, Weimiao Yu, Stephan Sanders
Software Mentions: 7
Published: almost 4 years ago

10.3389/fninf.2021.689675

Clinica: An Open-Source Software Platform for Reproducible Clinical Neuroscience Studies
Cited by: 47
Author(s): Alexandre Routier, Ninon Burgos, Mauricio Díaz, Michael Bacci, Simona Bottani, Omar El-Rifai, Sabrina Fontanella, Pietro Gori, Jérémy Guillon, A. Guyot, Ravi Hassanaly, Thomas Jacquemont, Pascal Lu, Arnaud Marcoux, T. Moreau, Jorge Samper‐Gonzàlez, Marc Teichmann, Elina Thibeau–Sutre, Ghislain Vaillant, Junhao Wen, Adam Wild, Marie‐Odile Habert, Stanley Durrleman, Olivier Colliot
Software Mentions: 6
Published: over 3 years ago

10.3389/fcell.2019.00141

Single Cell Imaging of Nuclear Architecture Changes
Cited by: 17
Author(s): Rikke Morrish, Michael Hermes, Jeremy Metz, Edwin M. Stone, Stefano Pagliara, Richard Chahwan, Francesca Palombo
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-021-90409-x

High-throughput phenotyping methods for quantifying hair fiber morphology
Cited by: 1
Author(s): Tina Lasisi, Arslan Zaidi, Timothy H. Webster, Nicholas Stephens, Kendall Routch, Nina G. Jablonski, Mark D. Shriver
Software Mentions: 6
Published: over 3 years ago

10.1016/j.cell.2016.09.027

Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells
Cited by: 620
Author(s): Gioele La Manno, Daniel Gyllborg, Simone Codeluppi, Kaneyasu Nishimura, Carmen Saltó, Amit Zeisel, Lars E. Borm, Simon Stott, Enrique M. Toledo, J. Carlos Villaescusa, Peter Lönnerberg, Jesper Ryge, Roger A. Barker, Ernest Arenas, Sten Linnarsson
Software Mentions: 6
Published: about 8 years ago

10.7554/eLife.48063

Initiation of chromosome replication controls both division and replication cycles in E. coli through a double-adder mechanism
Cited by: 44
Author(s): Guillaume Witz, Erik van Nimwegen, Thomas Julou
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pone.0203725

An open-source software analysis package for Microspheres with Ratiometric Barcode Lanthanide Encoding (MRBLEs)
Cited by: 15
Author(s): Björn Harink, Huy Nguyen, Kurt S. Thorn, Polly M. Fordyce
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0240802

OrganoidTracker: Efficient cell tracking using machine learning and manual error correction
Cited by: 32
Author(s): Rutger Nico Ulbe Kok, Laetitia Hebert, Guizela Huelsz-Prince, Yvonne J. Goos, Xuan Zheng, Katarzyna Bożek, Greg J. Stephens, Sander J. Tans, Jeroen S. van Zon
Software Mentions: 6
Published: about 4 years ago

10.1186/s13007-020-00591-8

The BELT and phenoSEED platforms: shape and colour phenotyping of seed samples
Cited by: 18
Author(s): Keith Halcro, Kaitlin McNabb, Ashley Lockinger, Didier Socquet-Juglard, Kirstin E. Bett, Scott D. Noble
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pcbi.1007973

XDream: Finding preferred stimuli for visual neurons using generative networks and gradient-free optimization
Cited by: 9
Author(s): Will Xiao, Gabriel Kreiman
Software Mentions: 6
Published: over 4 years ago

10.1186/s12859-018-2477-7

pyHIVE, a health-related image visualization and engineering system using Python
Cited by: 5
Author(s): Ruochi Zhang, Ruxing Zhao, Xinyang Zhao, Di Wu, Weiwei Zheng, Xin Feng, Fengfeng Zhou
Software Mentions: 6
Published: almost 6 years ago

10.7554/eLife.51085

CytoCensus, mapping cell identity and division in tissues and organs using machine learning
Cited by: 12
Author(s): Martin Hailstone, Dominic Waithe, Tamsin J Samuels, Yang Lu, Ita Costello, Yoav Arava, Elizabeth J. Robertson, Richard M. Parton, Ilan Davis
Software Mentions: 6
Published: over 4 years ago

10.3389/fpls.2021.715309

An Affordable Image-Analysis Platform to Accelerate Stomatal Phenotyping During Microscopic Observation
Cited by: 2
Author(s): Yosuke Toda, Toshiaki Tameshige, Masakazu Tomiyama, Toshinori Kinoshita, Kentaro Shimizu
Software Mentions: 6
Published: over 3 years ago

10.3389/fninf.2014.00034

Graph-based active learning of agglomeration (GALA): a Python library to segment 2D and 3D neuroimages
Cited by: 45
Author(s): Juan Nunez-Iglesias, Ryan Kennedy, Stephen M. Plaza, Anirban Chakraborty, William T. Katz
Software Mentions: 6
Published: over 10 years ago

10.1038/s41598-017-17858-1

Machine Learning for Nuclear Mechano-Morphometric Biomarkers in Cancer Diagnosis
Cited by: 38
Author(s): Adityanarayanan Radhakrishnan, Karthik Damodaran, Ali C. Soylemezoglu, Caroline Uhler, G. V. Shivashankar
Software Mentions: 5
Published: almost 7 years ago

10.1186/s12859-020-03661-9

METROID: an automated method for robust quantification of subcellular fluorescence events at low SNR
Cited by: 0
Author(s): Marcelo Zoccoler, Pedro Xavier de Oliveira
Software Mentions: 5
Published: over 4 years ago

10.1186/s12859-019-3004-1

mycelyso – high-throughput analysis of Streptomyces mycelium live cell imaging data
Cited by: 3
Author(s): Christian Carsten Sachs, Joachim Koepff, Wolfgang Wiechert, Alexander Grünberger, Katharina Nöh
Software Mentions: 5
Published: about 5 years ago

10.1186/s12859-017-1934-z

ImageJ2: ImageJ for the next generation of scientific image data
Cited by: 4,051
Author(s): Curtis Rueden, Johannes Schindelin, Mark Hiner, Barry E. DeZonia, Alison E. Walter, Ellen T. Arena, Kevin W. Eliceiri
Software Mentions: 5
Published: almost 7 years ago

10.1186/s12859-019-3055-3

Cytokit: a single-cell analysis toolkit for high dimensional fluorescent microscopy imaging
Cited by: 38
Author(s): Eric Czech, Bülent Arman Aksoy, Pınar Aksoy, Jeff Hammerbacher
Software Mentions: 5
Published: about 5 years ago

10.7717/peerj.4312

A new Python library to analyse skeleton images confirms malaria parasite remodelling of the red blood cell membrane skeleton
Cited by: 34
Author(s): Juan Nunez-Iglesias, Adam J. Blanch, Oliver Looker, Matthew W. A. Dixon, Leann Tilley
Software Mentions: 5
Published: almost 7 years ago

10.1371/journal.pcbi.1009274

Validation and tuning of in situ transcriptomics image processing workflows with crowdsourced annotations
Cited by: 0
Author(s): Jenny M. Vo-Phamhi, Kevin A. Yamauchi, Rafael Gómez-Sjöberg
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0215137

Quanfima: An open source Python package for automated fiber analysis of biomaterials
Cited by: 14
Author(s): Roman Shkarin, Andrei Shkarin, Svetlana Shkarina, A. Cecilia, Roman A. Surmenev, Venera Weinhardt, Tilo Baumbach, Ralf Mikut
Software Mentions: 5
Published: over 5 years ago

10.3390/cancers13051097

Functional States in Tumor-Initiating Cell Differentiation in Human Colorectal Cancer
Cited by: 10
Author(s): Martina K. Zowada, Stephan M. Tirier, Sebastian M. Dieter, Teresa G Krieger, Ava Oberlack, Robert Lorenz Chua, Mario Huerta, Foo Wei Ten, Karin Laaber, Jeongbin Park, Katharina Jechow, Torsten Müller, Mathias Kalxdorf, Mark Kriegsmann, Katharina Kriegsmann, Friederike Herbst, Jeroen Krijgsveld, Martin Schneider, Roland Eils, Hanno Glimm, Christian Conrad, Claudia R. Ball
Software Mentions: 5
Published: over 3 years ago

10.1016/j.compbiomed.2015.12.002

Rapid development of image analysis research tools: Bridging the gap between researcher and clinician with pyOsiriX
Cited by: 33
Author(s): Matthew Blackledge, David J. Collins, Dow‐Mu Koh, Martin O. Leach
Software Mentions: 5
Published: almost 9 years ago

10.3389/fonc.2020.531476

Application of MRI Radiomics-Based Machine Learning Model to Improve Contralateral BI-RADS 4 Lesion Assessment
Cited by: 11
Author(s): Hao Wen, Jing Gong, Shengping Wang, Hui Zhu, Bin Zhao, Weijun Peng
Software Mentions: 5
Published: about 4 years ago

10.1107/S2052252517006212

Healing X-ray scattering images
Cited by: 10
Author(s): Jiliang Liu, Julien Lhermitte, Ye Tian, Zheng Zhang, D. Yu, Kevin G. Yager
Software Mentions: 5
Published: over 7 years ago

10.1155/2021/1102083

Classification Framework for Healthy Hairs and Alopecia Areata: A Machine Learning (ML) Approach
Cited by: 10
Author(s): Choudhary Sobhan Shakeel, Saad Jawaid Khan, Beenish Moalla Chaudhry, Syeda Fatima Aijaz, Umer Hassan
Software Mentions: 4
Published: over 3 years ago

10.7554/eLife.40162

Motion sensing superpixels (MOSES) is a systematic computational framework to quantify and discover cellular motion phenotypes
Cited by: 8
Author(s): Felix Zhou, Carlos Ruiz‐Puig, Richard Owen, Michael J. White, Jens Rittscher, Xin Lü
Software Mentions: 4
Published: over 5 years ago

10.3389/fendo.2021.714561

Biased Coupling to β-Arrestin of Two Common Variants of the CB2 Cannabinoid Receptor
Cited by: 9
Author(s): Gábor Turu, Eszter Soltész‐Katona, András Tóth, C.C. Juhasz, Miklós Cserző, Ádám Misák, András Balla, Marc G. Caron, László Hunyady
Software Mentions: 4
Published: over 3 years ago

10.1242/bio.052936

A fully automated deep learning pipeline for high-throughput colony segmentation and classification
Cited by: 4
Author(s): Sarah H. Carl, Lea Duempelmann, Yukiko Shimada, Marc Bühler
Software Mentions: 4
Published: over 4 years ago

10.34133/2020/5839856

“Macrobot”: An Automated Segmentation-Based System for Powdery Mildew Disease Quantification
Cited by: 15
Author(s): Stefanie Lück, Marc Strickert, Maximilian Lorbeer, Friedrich Melchert, Andreas Backhaus, David Kilias, Udo Seiffert, Dimitar Douchkov
Software Mentions: 4
Published: almost 5 years ago

10.1107/S1600576719005363

ClickX: a visualization-based program for preprocessing of serial crystallography data
Cited by: 4
Author(s): Xuanxuan Li, Chufeng Li, Haiguang Liu
Software Mentions: 4
Published: over 5 years ago

10.1364/OE.401117

Microscope-AOtools: a generalised adaptive optics implementation
Cited by: 10
Author(s): Nicholas Hall, Josh Titlow, Martin J. Booth, Ian M. Dobbie
Software Mentions: 4
Published: about 4 years ago

10.7554/eLife.38173

CaImAn an open source tool for scalable calcium imaging data analysis
Cited by: 495
Author(s): Andrea Giovannucci, Johannes Friedrich, Pat Gunn, Jérémie Kalfon, Brandon Brown, S. A. Koay, Jiannis Taxidis, Farzaneh Najafi, Jeffrey Gauthier, Pengcheng Zhou, Baljit S. Khakh, David W. Tank, Dmitri B. Chklovskii, Eftychios A. Pnevmatikakis
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0195747

UXT is required for spermatogenesis in mice
Cited by: 5
Author(s): Eric D. Schafler, Phillip A. Thomas, Susan Ha, Yu Wang, Keria Bermudez-Hernandez, Zuojian Tang, David Fenyö, Margarita Vigodner, Susan K. Logan
Software Mentions: 4
Published: over 6 years ago

10.7554/eLife.59780

On the objectivity, reliability, and validity of deep learning enabled bioimage analyses
Cited by: 25
Author(s): Dennis Segebarth, Matthias Griebel, Nikolai Stein, Cora R. von Collenberg, Corinna Martin, Dominik Fiedler, Lucas B. Comeras, Anupam Sah, Victoria Schoeffler, Teresa M. Lüffe, Alexander Dürr, Rohini Gupta, Manju Sasi, Christina Lillesaar, Maren D. Lange, Ramon Tasan, Nicolas Singewald, Hans‐Christian Pape, Christoph M. Flath, Robert Blum
Software Mentions: 4
Published: about 4 years ago

10.1021/acsnano.0c10632

Spatial Regulation of T-Cell Signaling by Programmed Death-Ligand 1 on Wireframe DNA Origami Flat Sheets
Cited by: 37
Author(s): Trixy Fang, Jonatan Alvelid, Joel Spratt, Elena Ambrosetti, Ilaria Testa, Ana I. Teixeira
Software Mentions: 4
Published: almost 4 years ago

10.3390/e21121168

Using Entropy for Welds Segmentation and Evaluation
Cited by: 7
Author(s): Oto Haffner, Erik Kučera, Peter Drahoš, Jan Cigánek
Software Mentions: 4
Published: almost 5 years ago

10.1038/s42003-021-02166-2

Spatially visualized single-cell pathology of highly multiplexed protein profiles in health and disease
Cited by: 5
Author(s): Mayar Allam, Thomas Hu, Shuangyi Cai, Krishnan Laxminarayanan, Robert B. Hughley, Ahmet F. Coşkun
Software Mentions: 4
Published: over 3 years ago

10.7717/peerj.4088

PlantCV v2: Image analysis software for high-throughput plant phenotyping
Cited by: 191
Author(s): Malia Gehan, Arash Abbasi, Jeffrey C. Berry, Steven T. Callen, Leonardo Chavez, Andrew N. Doust, Max Feldman, Kerrigan B. Gilbert, John G. Hodge, J. Steen Hoyer, Andy Lin, Suxing Liu, César Lizárraga, Argelia Lorence, Michael D. Miller, Éric Platon, Monica Tessman, Tony Sax
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12859-020-3526-6

Substitution matrix based color schemes for sequence alignment visualization
Cited by: 3
Author(s): Patrick Kunzmann, Benjamin E. Mayer, Kay Hamacher
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-020-74500-3

SHIFT: speedy histological-to-immunofluorescent translation of a tumor signature enabled by deep learning
Cited by: 25
Author(s): Erik Burlingame, Mary McDonnell, Geoffrey F. Schau, Guillaume Thibault, Christian Lanciault, Terry K. Morgan, Brett Johnson, Christopher L. Corless, Joe W. Gray, Young Hwan Chang
Software Mentions: 4
Published: about 4 years ago

10.3390/app10186187

ACDC: Automated Cell Detection and Counting for Time-Lapse Fluorescence Microscopy
Cited by: 7
Author(s): Leonardo Rundo, Andrea Tangherloni, Darren R. Tyson, Riccardo Betta, Carmelo Militello, Simone Spolaor, Marco S. Nobile, Daniela Besozzi, Alexander L R Lubbock, Vito Quaranta, Giancarlo Mauri, Carlos F. López, Paolo Cazzaniga
Software Mentions: 4
Published: about 4 years ago

10.3389/fcell.2020.00350

Localization Preference of Antimicrobial Peptides on Liquid-Disordered Membrane Domains
Cited by: 26
Author(s): Juanjuan Su, Siewert J. Marrink, Manuel N. Melo
Software Mentions: 3
Published: over 4 years ago

10.7717/peerj.11155

<i>scAnt</i>—an open-source platform for the creation of 3D models of arthropods (and other small objects)
Cited by: 10
Author(s): Fabian Plum, David Labonte
Software Mentions: 3
Published: over 3 years ago

10.1083/jcb.202003052

Stochastic combinations of actin regulatory proteins are sufficient to drive filopodia formation
Cited by: 15
Author(s): Ulrich Dobramysl, Iris K. Jarsch, Yoshiko Inoue, Hanae Shimo, Benjamin Richier, Jonathan R Gadsby, Julia Mason, Alicja M. Szalapak, Pantelis Savvas Ioannou, Guilherme Pereira Correia, Astrid Walrant, Richard J. Butler, Édouard Hannezo, Benjamin D. Simons, Jennifer L. Gallop
Software Mentions: 3
Published: over 3 years ago

10.1038/s42003-021-01786-y

Whole-organ analysis of TGF-β-mediated remodelling of the tumour microenvironment by tissue clearing
Cited by: 12
Author(s): Shimpei I. Kubota, Kei Takahashi, Tomoyuki Mano, Katsuhiko Matsumoto, Takahiro Katsumata, Shoi Shi, Kazuki Tainaka, Hiroki R. Ueda, Shogo Ehata, Kohei Miyazono
Software Mentions: 3
Published: over 3 years ago

10.1017/cts.2020.531

Developing image analysis pipelines of whole-slide images: Pre- and post-processing
Cited by: 12
Author(s): Byron H. Smith, Meyke Hermsen, Elizabeth R. Lesser, Deepak Ravichandar, Walter K. Kremers
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pcbi.1008007

Nine quick tips for efficient bioinformatics curriculum development and training
Cited by: 3
Author(s): Susan McClatchy, Kristin M. Bass, Daniel M. Gatti, Adam Moylan, Gary A. Churchill
Software Mentions: 3
Published: over 4 years ago

10.1242/dmm.047001

Transformed notochordal cells trigger chronic wounds in zebrafish, destabilizing the vertebral column and bone homeostasis
Cited by: 7
Author(s): Paco López-Cuevas, Luke Deane, Yuan Yang, Chrissy L. Hammond, Érika Kague
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-021-89848-3

A deep learning model for detection of cervical spinal cord compression in MRI scans
Cited by: 26
Author(s): Zamir Merali, Justin Z Wang, Jetan H. Badhiwala, Christopher D. Witiw, Jefferson R. Wilson, Michael G. Fehlings
Software Mentions: 3
Published: over 3 years ago

10.1007/s12559-017-9536-7

Evaluating Integration Strategies for Visuo-Haptic Object Recognition
Cited by: 12
Author(s): Sibel Toprak, Nicolás Navarro-Guerrero, Stefan Wermter
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0252505

Statistical image analysis and escort histograms in characterization of articular cartilage repair in a skeleton animal model
Cited by: 0
Author(s): Ryszard Tomaszewski, Jerzy Dajka
Software Mentions: 3
Published: over 3 years ago

10.3390/s21103465

SpeakingFaces: A Large-Scale Multimodal Dataset of Voice Commands with Visual and Thermal Video Streams
Cited by: 27
Author(s): Madina Abdrakhmanova, Askat Kuzdeuov, Sheikh Jarju, Yerbolat Khassanov, Michael D. Lewis, Hüseyin Atakan Varol
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-021-87644-7

A deep learning model for the classification of indeterminate lung carcinoma in biopsy whole slide images
Cited by: 19
Author(s): Fahdi Kanavati, Gouji Toyokawa, Seiya Momosaki, Hiroaki Takeoka, Masaki Okamoto, Koji Yamazaki, Sadanori Takeo, Osamu Iizuka, Masayuki Tsuneki
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pcbi.1006628

Performance of convolutional neural networks for identification of bacteria in 3D microscopy datasets
Cited by: 46
Author(s): Edouard A. Hay, Raghuveer Parthasarathy
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-021-94862-6

Tumor collagen framework from bright-field histology images predicts overall survival of breast carcinoma patients
Cited by: 3
Author(s): Mindaugas Morkūnas, Dovile Zilenaite, Aida Laurinavičienė, Povilas Treigys, Arvydas Laurinavičius
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-020-62997-7

Dynamic spherical harmonics approach for shape classification of migrating cells
Cited by: 29
Author(s): Anna Medyukhina, Marco Blickensdorf, Zoltán Cseresnyés, Nora Ruef, Jens V Stein, Marc Thilo Figge
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-021-87557-5

Efficient few-shot machine learning for classification of EBSD patterns
Cited by: 15
Author(s): Kevin Kaufmann, Hobson Lane, Xiao Liu, Kenneth S. Vecchio
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-019-44839-3

Deep Learning for the Radiographic Detection of Periodontal Bone Loss
Cited by: 199
Author(s): Joachim Krois, Thomas Ekert, Leonie Meinhold, Tatiana Golla, Basel Kharbot, Agnes Wittemeier, Christof E. Dörfer, Falk Schwendicke
Software Mentions: 3
Published: over 5 years ago

10.3390/ma13081887

A Novel Approach to Discrete Representative Volume Element Automation and Generation-DRAGen
Cited by: 11
Author(s): Manuel Henrich, Felix Pütz, Sebastian Münstermann
Software Mentions: 3
Published: over 4 years ago

10.1093/gigascience/giz143

Accessible and reproducible mass spectrometry imaging data analysis in Galaxy
Cited by: 16
Author(s): Melanie Christine Föll, Lennart Moritz, Thomas Wollmann, Maren Nicole Stillger, Niklas Vockert, Martin Werner, Peter Bronsert, Karl Rohr, Björn Grüning, Oliver Schilling
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12903-021-01551-x

Automated segmentation and description of the internal morphology of human permanent teeth by means of micro-CT
Cited by: 3
Author(s): David Haberthür, Ruslan Hlushchuk, Thomas Gerhard Wolf
Software Mentions: 3
Published: over 3 years ago

10.7717/peerj.6652

IOCBIO Sparks detection and analysis software
Cited by: 9
Author(s): Martin Laasmaa, Niina Karro, Rikke Birkedal, Marko Vendelin
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pgen.1008337

A first genetic portrait of synaptonemal complex variation
Cited by: 18
Author(s): Richard J. Wang, Beth L. Dumont, Peicheng Jing, Bret A. Payseur
Software Mentions: 3
Published: about 5 years ago

10.3390/s20174819

Polylidar3D-Fast Polygon Extraction from 3D Data
Cited by: 5
Author(s): Jeremy D. Castagno, Ella M. Atkins
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0167356

A Novel Microfluidic Assay for Rapid Phenotypic Antibiotic Susceptibility Testing of Bacteria Detected in Clinical Blood Cultures
Cited by: 33
Author(s): Christer Malmberg, Pikkei Yuen, Johanna Spaak, Otto Cars, Thomas Tängdén, Pernilla Lagerbäck
Software Mentions: 3
Published: almost 8 years ago

10.1107/S1600576718015145

High-throughput continuous rotation electron diffraction data acquisition<i>via</i>software automation
Cited by: 110
Author(s): Magdalena Ola Cichocka, Jonas Ångström, Bin Wang, Xiaodong Zou, Stef Smeets
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-020-77549-2

Automated measurement of long-term bower behaviors in Lake Malawi cichlids using depth sensing and action recognition
Cited by: 3
Author(s): Zachary V. Johnson, Manu Tej Sharma Arrojwala, Vineeth Aljapur, Tyrone Lee, Tucker J. Lancaster, Mark C. Lowder, Karen Gu, Joseph Stockert, Rachel L. Lecesne, Jean Michael Moorman, J. Todd Streelman, Patrick T. McGrath
Software Mentions: 3
Published: almost 4 years ago

10.3389/fonc.2019.00821

CT-Based Radiomics Signature for the Preoperative Discrimination Between Head and Neck Squamous Cell Carcinoma Grades
Cited by: 36
Author(s): Wenli Wu, Junyong Ye, Qi Wang, Jin Luo, Shengsheng Xu
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-020-69730-4

Three-dimensional bright-field microscopy with isotropic resolution based on multi-view acquisition and image fusion reconstruction
Cited by: 5
Author(s): Gianmaria Calisesi, Alessia Candeo, Andrea Farina, Cosimo D’Andrea, V. Magni, Gianluca Valentini, Anna Pistocchi, Alex Costa, Andrea Bassi
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-020-74599-4

Texture features from computed tomography correlate with markers of severity in acute alcohol-associated hepatitis
Cited by: 5
Author(s): Michele M. Tana, David McCoy, Briton Lee, Roshan Patel, Joseph A. Lin, Michael A. Ohliger
Software Mentions: 2
Published: about 4 years ago

10.34133/2020/3194308

A Deep Learning-Based Phenotypic Analysis of Rice Root Distribution from Field Images
Cited by: 20
Author(s): Shota Teramoto, Yusaku Uga
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0082710

An Automated Blur Detection Method for Histological Whole Slide Imaging
Cited by: 29
Author(s): Xavier Moles Lopez, Etienne D'Andrea, Paul Barbot, Anne-Sophie Bridoux, Sandrine Rorive, Isabelle Salmon, Olivier Debeir, Christine Decaestecker
Software Mentions: 2
Published: almost 11 years ago

10.1038/s41598-021-87882-9

A prognostic dynamic model applicable to infectious diseases providing easily visualized guides: a case study of COVID-19 in the UK
Cited by: 2
Author(s): Yuxuan Zhang, Chen Gong, Dawei Li, Zhiwei Wang, Shengda D. Pu, Alex W. Robertson, Hong Yu, John Parrington
Software Mentions: 2
Published: over 3 years ago

10.1039/c3fd00131h

NRas slows the rate at which a model lipid bilayer phase separates
Cited by: 17
Author(s): Elizabeth Jefferys, Mark S.P. Sansom, Philip W. Fowler
Software Mentions: 2
Published: almost 11 years ago

10.1038/s41598-021-90444-8

A generalized deep learning framework for whole-slide image segmentation and analysis
Cited by: 64
Author(s): Mahendra Khened, Avinash Kori, Haran Rajkumar, Ganapathy Krishnamurthi, Balaji Vasan Srinivasan
Software Mentions: 2
Published: over 3 years ago

Projects: pypi: scikit-image

Papers Mentioning scikit-image 195