Literature DB >> 30065368

Quanti.us: a tool for rapid, flexible, crowd-based annotation of images.

Alex J Hughes1,2,3, Joseph D Mornin4, Sujoy K Biswas2,5, Lauren E Beck3, David P Bauer2,6, Arjun Raj3, Simone Bianco2,5, Zev J Gartner7,8,9.   

Abstract

We describe Quanti.us , a crowd-based image-annotation platform that provides an accurate alternative to computational algorithms for difficult image-analysis problems. We used Quanti.us for a variety of medium-throughput image-analysis tasks and achieved 10-50× savings in analysis time compared with that required for the same task by a single expert annotator. We show equivalent deep learning performance for Quanti.us-derived and expert-derived annotations, which should allow scalable integration with tailored machine learning algorithms.

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Mesh:

Year:  2018        PMID: 30065368      PMCID: PMC8863499          DOI: 10.1038/s41592-018-0069-0

Source DB:  PubMed          Journal:  Nat Methods        ISSN: 1548-7091            Impact factor:   28.547


  13 in total

1.  Detecting overlapping instances in microscopy images using extremal region trees.

Authors:  Carlos Arteta; Victor Lempitsky; J Alison Noble; Andrew Zisserman
Journal:  Med Image Anal       Date:  2015-04-14       Impact factor: 8.545

Review 2.  Deep learning.

Authors:  Yann LeCun; Yoshua Bengio; Geoffrey Hinton
Journal:  Nature       Date:  2015-05-28       Impact factor: 49.962

3.  Multimotor transport in a system of active and inactive kinesin-1 motors.

Authors:  Lara Scharrel; Rui Ma; René Schneider; Frank Jülicher; Stefan Diez
Journal:  Biophys J       Date:  2014-07-15       Impact factor: 4.033

4.  TrackMate: An open and extensible platform for single-particle tracking.

Authors:  Jean-Yves Tinevez; Nick Perry; Johannes Schindelin; Genevieve M Hoopes; Gregory D Reynolds; Emmanuel Laplantine; Sebastian Y Bednarek; Spencer L Shorte; Kevin W Eliceiri
Journal:  Methods       Date:  2016-10-03       Impact factor: 3.608

5.  Dermatologist-level classification of skin cancer with deep neural networks.

Authors:  Andre Esteva; Brett Kuprel; Roberto A Novoa; Justin Ko; Susan M Swetter; Helen M Blau; Sebastian Thrun
Journal:  Nature       Date:  2017-01-25       Impact factor: 49.962

6.  A subcellular map of the human proteome.

Authors:  Peter J Thul; Lovisa Åkesson; Mikaela Wiking; Diana Mahdessian; Aikaterini Geladaki; Hammou Ait Blal; Tove Alm; Anna Asplund; Lars Björk; Lisa M Breckels; Anna Bäckström; Frida Danielsson; Linn Fagerberg; Jenny Fall; Laurent Gatto; Christian Gnann; Sophia Hober; Martin Hjelmare; Fredric Johansson; Sunjae Lee; Cecilia Lindskog; Jan Mulder; Claire M Mulvey; Peter Nilsson; Per Oksvold; Johan Rockberg; Rutger Schutten; Jochen M Schwenk; Åsa Sivertsson; Evelina Sjöstedt; Marie Skogs; Charlotte Stadler; Devin P Sullivan; Hanna Tegel; Casper Winsnes; Cheng Zhang; Martin Zwahlen; Adil Mardinoglu; Fredrik Pontén; Kalle von Feilitzen; Kathryn S Lilley; Mathias Uhlén; Emma Lundberg
Journal:  Science       Date:  2017-05-11       Impact factor: 47.728

7.  A rapid and efficient 2D/3D nuclear segmentation method for analysis of early mouse embryo and stem cell image data.

Authors:  Xinghua Lou; Minjung Kang; Panagiotis Xenopoulos; Silvia Muñoz-Descalzo; Anna-Katerina Hadjantonakis
Journal:  Stem Cell Reports       Date:  2014-03-11       Impact factor: 7.765

8.  Space-time wiring specificity supports direction selectivity in the retina.

Authors:  Jinseop S Kim; Matthew J Greene; Aleksandar Zlateski; Kisuk Lee; Mark Richardson; Srinivas C Turaga; Michael Purcaro; Matthew Balkam; Amy Robinson; Bardia F Behabadi; Michael Campos; Winfried Denk; H Sebastian Seung
Journal:  Nature       Date:  2014-05-04       Impact factor: 49.962

9.  Automated Training of Deep Convolutional Neural Networks for Cell Segmentation.

Authors:  Sajith Kecheril Sadanandan; Petter Ranefall; Sylvie Le Guyader; Carolina Wählby
Journal:  Sci Rep       Date:  2017-08-10       Impact factor: 4.379

10.  Nanoscale imaging of RNA with expansion microscopy.

Authors:  Fei Chen; Asmamaw T Wassie; Allison J Cote; Anubhav Sinha; Shahar Alon; Shoh Asano; Evan R Daugharthy; Jae-Byum Chang; Adam Marblestone; George M Church; Arjun Raj; Edward S Boyden
Journal:  Nat Methods       Date:  2016-07-04       Impact factor: 28.547

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  13 in total

1.  Scientific Discovery Games for Biomedical Research.

Authors:  Rhiju Das; Benjamin Keep; Peter Washington; Ingmar H Riedel-Kruse
Journal:  Annu Rev Biomed Data Sci       Date:  2019-07

Review 2.  Pathological Response and Immune Biomarker Assessment in Non-Small-Cell Lung Carcinoma Receiving Neoadjuvant Immune Checkpoint Inhibitors.

Authors:  Frank Rojas; Edwin Roger Parra; Ignacio Ivan Wistuba; Cara Haymaker; Luisa Maren Solis Soto
Journal:  Cancers (Basel)       Date:  2022-06-02       Impact factor: 6.575

Review 3.  Deep learning for cellular image analysis.

Authors:  Erick Moen; Dylan Bannon; Takamasa Kudo; William Graf; Markus Covert; David Van Valen
Journal:  Nat Methods       Date:  2019-05-27       Impact factor: 28.547

Review 4.  Introduction to Digital Image Analysis in Whole-slide Imaging: A White Paper from the Digital Pathology Association.

Authors:  Famke Aeffner; Mark D Zarella; Nathan Buchbinder; Marilyn M Bui; Matthew R Goodman; Douglas J Hartman; Giovanni M Lujan; Mariam A Molani; Anil V Parwani; Kate Lillard; Oliver C Turner; Venkata N P Vemuri; Ana G Yuil-Valdes; Douglas Bowman
Journal:  J Pathol Inform       Date:  2019-03-08

5.  Advancing computational biology and bioinformatics research through open innovation competitions.

Authors:  Andrea Blasco; Michael G Endres; Rinat A Sergeev; Anup Jonchhe; N J Maximilian Macaluso; Rajiv Narayan; Ted Natoli; Jin H Paik; Bryan Briney; Chunlei Wu; Andrew I Su; Aravind Subramanian; Karim R Lakhani
Journal:  PLoS One       Date:  2019-09-27       Impact factor: 3.240

6.  Evaluation of Deep Learning Strategies for Nucleus Segmentation in Fluorescence Images.

Authors:  Juan C Caicedo; Jonathan Roth; Allen Goodman; Tim Becker; Kyle W Karhohs; Matthieu Broisin; Csaba Molnar; Claire McQuin; Shantanu Singh; Fabian J Theis; Anne E Carpenter
Journal:  Cytometry A       Date:  2019-07-16       Impact factor: 4.355

7.  Structured crowdsourcing enables convolutional segmentation of histology images.

Authors:  Mohamed Amgad; Habiba Elfandy; Hagar Hussein; Lamees A Atteya; Mai A T Elsebaie; Lamia S Abo Elnasr; Rokia A Sakr; Hazem S E Salem; Ahmed F Ismail; Anas M Saad; Joumana Ahmed; Maha A T Elsebaie; Mustafijur Rahman; Inas A Ruhban; Nada M Elgazar; Yahya Alagha; Mohamed H Osman; Ahmed M Alhusseiny; Mariam M Khalaf; Abo-Alela F Younes; Ali Abdulkarim; Duaa M Younes; Ahmed M Gadallah; Ahmad M Elkashash; Salma Y Fala; Basma M Zaki; Jonathan Beezley; Deepak R Chittajallu; David Manthey; David A Gutman; Lee A D Cooper
Journal:  Bioinformatics       Date:  2019-09-15       Impact factor: 6.937

Review 8.  Computational pathology definitions, best practices, and recommendations for regulatory guidance: a white paper from the Digital Pathology Association.

Authors:  Esther Abels; Liron Pantanowitz; Famke Aeffner; Mark D Zarella; Jeroen van der Laak; Marilyn M Bui; Venkata Np Vemuri; Anil V Parwani; Jeff Gibbs; Emmanuel Agosto-Arroyo; Andrew H Beck; Cleopatra Kozlowski
Journal:  J Pathol       Date:  2019-09-03       Impact factor: 7.996

9.  EVICAN-a balanced dataset for algorithm development in cell and nucleus segmentation.

Authors:  Mischa Schwendy; Ronald E Unger; Sapun H Parekh
Journal:  Bioinformatics       Date:  2020-06-01       Impact factor: 6.937

10.  A fully automated deep learning pipeline for high-throughput colony segmentation and classification.

Authors:  Sarah H Carl; Lea Duempelmann; Yukiko Shimada; Marc Bühler
Journal:  Biol Open       Date:  2020-06-23       Impact factor: 2.422

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