pypi: Watershed | Projects | Ecosyste.ms: Papers

10.1186/s12915-021-01086-1

A phenomics approach for antiviral drug discovery
Cited by: 10
Author(s): Jonne Rietdijk, Marianna Tampere, Aleksandra Pettke, Polina Georgiev, Maris Lapins, Ulrika Warpman Berglund, Ola Spjuth, Marjo-Riitta Puumalainen, Jordi Carreras-Puigvert
Software Mentions: 6
Published: over 3 years ago

10.7554/eLife.40197

Global DNA methylation remodeling during direct reprogramming of fibroblasts to neurons
Cited by: 61
Author(s): Chongyuan Luo, Qian Yi Lee, Orly L. Wapinski, Rosa Castanon, Joseph R. Nery, Moritz Mall, Michael S. Kareta, Shay Cullen, Margaret A. Goodell, Howard Y. Chang, Marius Wernig, Joseph R. Ecker
Software Mentions: 6
Published: almost 6 years ago

10.7554/eLife.58123

TBX3 acts as tissue-specific component of the Wnt/β-catenin transcriptional complex
Cited by: 28
Author(s): Dario Zimmerli, Costanza Borrelli, Amaia Jauregi-Miguel, Simon Söderholm, Salome Brütsch, Nikolaos Doumpas, Jan Reichmuth, Fabienne Murphy-Seiler, Michel Aguet, Konrad Basler, Andreas E. Moor, Claudio Cantù
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pgen.1009512

The actin nucleation factors JMY and WHAMM enable a rapid Arp2/3 complex-mediated intrinsic pathway of apoptosis
Cited by: 11
Author(s): Virginia L King, Nathan K. Leclair, Alyssa Coulter, Kenneth Campellone
Software Mentions: 4
Published: over 3 years ago

10.7554/eLife.57000

Subcellular sorting of neuregulins controls the assembly of excitatory-inhibitory cortical circuits
Cited by: 18
Author(s): David Exposito-Alonso, Catarina Osório, C. Bernard, Sandra Pascual-García, Isabel del Pino, Òscar Marín, Beatriz Rico
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pntd.0003298

Topography and Land Cover of Watersheds Predicts the Distribution of the Environmental Pathogen Mycobacterium ulcerans in Aquatic Insects
Cited by: 13
Author(s): Kevin Carolan, Andrés Garchitorena, Gabriel E. García‐Peña, Aaron L. Morris, Jordi Landier, Arnaud Fontanet, Philippe Gall, Gaétan Texier, Laurent Marsollier, Rodolphe E. Gozlan, Sara Eyangoh, Danny Lo Seen, Jean‐François Guégan
Software Mentions: 3
Published: about 10 years ago

10.1186/s12915-019-0633-9

Analysis of sea star larval regeneration reveals conserved processes of whole-body regeneration across the metazoa
Cited by: 36
Author(s): Gregory A. Cary, Andrew Wolff, Olga Zueva, Joseph Pattinato
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-021-86912-w

PathoNet introduced as a deep neural network backend for evaluation of Ki-67 and tumor-infiltrating lymphocytes in breast cancer
Cited by: 23
Author(s): Farzin Negahbani, Rasool Sabzi, Bita Pakniyat Jahromi, Dena Firouzabadi, Fateme Movahedi, Mahsa Kohandel‐Shirazi, Shayan Majidi, Amirreza Dehghanian
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0020148

Simultaneous Visualization of Both Signaling Cascade Activity and End-Point Gene Expression in Single Cells
Cited by: 14
Author(s): Irene Weibrecht, Ida Grundberg, Mats Nilsson, Ola Söderberg
Software Mentions: 2
Published: over 13 years ago

10.3390/cancers13081777

SIO: A Spatioimageomics Pipeline to Identify Prognostic Biomarkers Associated with the Ovarian Tumor Microenvironment
Cited by: 12
Author(s): Ying Zhu, Sammy Ferri-Borgogno, Jianting Sheng, Tsz-Lun Yeung, Jared K. Burks, Paola Cappello, Amir A. Jazaeri, Jae Hoon Kim, Gwan Hee Han, Michael J. Birrer, Samuel C. Mok, Stephen T.C. Wong
Software Mentions: 2
Published: over 3 years ago

10.1186/s13068-018-1095-y

Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics
Cited by: 16
Author(s): Jason Whitham, Ji Won Moon, Miguel Rodríguez, Nancy L. Engle, Dawn M. Klingeman, Thomas Rydzak, Malaney M. Abel, Timothy J. Tschaplinski, Adam M. Guss, Steven D. Brown
Software Mentions: 2
Published: over 6 years ago

10.1186/s12859-015-0617-x

Robust and automated three-dimensional segmentation of densely packed cell nuclei in different biological specimens with Lines-of-Sight decomposition
Cited by: 42
Author(s): Biena Mathew, Alexander Schmitz, Silvia Muñoz-Descalzo, Nariman Ansari, Francesco Pampaloni, Ernst H. K. Stelzer, Sabine Fischer
Software Mentions: 2
Published: over 9 years ago

10.7554/eLife.59465

A single-cell atlas of the mouse and human prostate reveals heterogeneity and conservation of epithelial progenitors
Cited by: 58
Author(s): Laura Crowley, Francesco Cambuli, Luis Aparicio, Maho Shibata, Brian D. Robinson, Shouhong Xuan, Weiping Li, Hanina Hibshoosh, Massimo Loda, Raúl Rabadán, Michael M. Shen
Software Mentions: 2
Published: about 4 years ago

10.3389/fnana.2019.00098

Automated Individualization of Size-Varying and Touching Neurons in Macaque Cerebral Microscopic Images
Cited by: 8
Author(s): Zhenzhen You, Yaël Balbastre, Clément Bouvier, Anne‐Sophie Hérard, Pauline Gipchtein, Philippe Hantraye, Caroline Jan, Nicolas Souedet, Thierry Delzescaux
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0049127

Fibroblast Growth Factor 10-Fibroblast Growth Factor Receptor 2b Mediated Signaling Is Not Required for Adult Glandular Stomach Homeostasis
Cited by: 9
Author(s): Allison L. Speer, Denise Al Alam, F.G. Sala, Henri R. Ford, Savério Bellusci, Tracy C. Grikscheit
Software Mentions: 2
Published: about 12 years ago

10.3389/fncir.2016.00028

Modulation of Specific Sensory Cortical Areas by Segregated Basal Forebrain Cholinergic Neurons Demonstrated by Neuronal Tracing and Optogenetic Stimulation in Mice
Cited by: 28
Author(s): Irene Chaves-Coira, Natalí Barros-Zulaica, Margarita L. Rodrigo‐Angulo, Ángel Núñez
Software Mentions: 1
Published: over 8 years ago

10.3389/fnana.2013.00049

3D segmentations of neuronal nuclei from confocal microscope image stacks
Cited by: 17
Author(s): Antonio LaTorre, Lidia Alonso‐Nanclares, Santiago Muelas, José M. Peña, Javier DeFelipe
Software Mentions: 1
Published: almost 12 years ago

10.3389/fnins.2021.632768

Neuroskeletal Effects of Chronic Bioelectric Nerve Stimulation in Health and Diabetes
Cited by: 1
Author(s): Alec T Beeve, Ivana Shen, Xiao Zhang, Kristann Magee, Yan Yan, Matthew R. MacEwan, Erica L. Scheller
Software Mentions: 1
Published: over 3 years ago

10.3389/fpls.2016.00119

Precision Automation of Cell Type Classification and Sub-Cellular Fluorescence Quantification from Laser Scanning Confocal Images
Cited by: 20
Author(s): Hardy Hall, Azadeh Fakhrzadeh, Cris L. Luengo Hendriks, Urs Fischer
Software Mentions: 1
Published: almost 9 years ago

10.1186/2047-2501-1-5

Segmentation of ultrasound images of thyroid nodule for assisting fine needle aspiration cytology
Cited by: 26
Author(s): Jie Zhao, Wei Xing Zheng, Li Zhang, Huayu Tian
Software Mentions: 1
Published: almost 12 years ago

10.1007/s10278-021-00452-3

Semantic Instance Segmentation of Kidney Cysts in MR Images: A Fully Automated 3D Approach Developed Through Active Learning
Cited by: 10
Author(s): Adriana Gregory, Deema Anaam, Andrew J. Vercnocke, Marie E. Edwards, Vicente E. Torres, Peter C. Harris, Bradley J. Erickson, Timothy L. Kline
Software Mentions: 1
Published: over 3 years ago

10.1038/srep16002

A combined MR and CT study for precise quantitative analysis of the avian brain
Cited by: 6
Author(s): Daniel Jirák, Jiřı́ Janáček, Benjamin P. Kear
Software Mentions: 1
Published: about 9 years ago

10.1038/srep18734

Transgenic FingRs for Live Mapping of Synaptic Dynamics in Genetically-Defined Neurons
Cited by: 27
Author(s): Jong Hyun Son, Matthew D. Keefe, Tamara J. Stevenson, Joshua Barrios, Scott Anjewierden, James Newton, Adam D. Douglass, Joshua L. Bonkowsky
Software Mentions: 1
Published: almost 9 years ago

10.1038/srep32127

Automated Ki-67 Quantification of Immunohistochemical Staining Image of Human Nasopharyngeal Carcinoma Xenografts
Cited by: 33
Author(s): Peng Shi, Jing Zhong, Jinsheng Hong, Ruoxuan Huang, Kaijun Wang, Yunbin Chen
Software Mentions: 1
Published: about 8 years ago

10.1038/srep40285

Core Transcription Factors, MicroRNAs, and Small Molecules Drive Transdifferentiation of Human Fibroblasts Towards The Cardiac Cell Lineage
Cited by: 36
Author(s): Nicolas Christoforou, Samarshi Chakraborty, Robert D. Kirkton, Andrew F. Adler, Russell C. Addis, Kam W. Leong
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-018-22319-4

Radiomics Features Differentiate Between Normal and Tumoral High-Fdg Uptake
Cited by: 17
Author(s): Chih‐Yang Hsu, Mikhail Doubrovin, Chia‐Ho Hua, Omar J. Mohammed, Barry L. Shulkin, Sue C. Kaste, Sara M. Federico, M Metzger, Matthew J. Krasin, Christopher L. Tinkle, Thomas E. Merchant, John T. Lucas
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-018-33550-4

The consequences of porcine IVM medium supplementation with follicular fluid become reflected in embryo quality, yield and gene expression patterns
Cited by: 22
Author(s): Piotr Pawlak, Ewelina Warzych, Adam Cieślak, Natalia Małyszka, Eliza Maciejewska, Zofia E. Madeja, D. Lechniak
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-019-39760-8

High-throughput Evaluation of Protein Migration and Localization after Laser Micro-Irradiation
Cited by: 6
Author(s): Sebastian Oeck, Nathalie M. Malewicz, A. Krysztofiak, Audrey Turchick, Verena Jendrossek, Peter M. Glazer
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-019-38813-2

Segmentation of Heavily Clustered Nuclei from Histopathological Images
Cited by: 47
Author(s): Mahmoud Abdolhoseini, Murielle G. Kluge, Frederick R. Walker, Sarah J. Johnson
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-020-72248-4

Traceable stimulus-dependent rapid molecular changes in dendritic spines in the brain
Cited by: 2
Author(s): Kazuya Kuboyama, Takafumi Inoue, Yuki Hashimotodani, Takuya Itoh, Tohsuke Suzuki, Aya Tetsuzawa, Yosuke Ohtsuka, Ryô Kinoshita, Ren Takara, Tohru Miyazawa, Pooja Gusain, Masanobu Kano, Maki K. Yamada
Software Mentions: 1
Published: about 4 years ago

10.1038/s41598-021-91168-5

Capicua regulates the development of adult-born neurons in the hippocampus
Cited by: 3
Author(s): Brenna Hourigan, Spencer D. Balay, Graydon Yee, Saloni Sharma, Qingrong Tan
Software Mentions: 1
Published: over 3 years ago

10.1093/humrep/deaa205

The duration of embryo culture after mouse IVF differentially affects cardiovascular and metabolic health in male offspring
Cited by: 23
Author(s): Anan Aljahdali, R. K. Raja Ili Airina, Miguel A. Velazquez, Bhavwanti Sheth, Katrina R. Wallen, Clive Osmond, Adam Watkins, Judith Eckert, Neil Smyth, Tom P. Fleming
Software Mentions: 1
Published: about 4 years ago

10.3390/jimaging5040043

Knee-Cartilage Segmentation and Thickness Measurement from 2D Ultrasound
Cited by: 11
Author(s): Prajna Ramesh Desai, Ilker Hacihaliloglu
Software Mentions: 1
Published: over 5 years ago

10.3390/jimaging6070072

Edge-Based Color Image Segmentation Using Particle Motion in a Vector Image Field Derived from Local Color Distance Images
Cited by: 4
Author(s): Wutthichai Phornphatcharaphong, Nawapak Eua-Anant
Software Mentions: 1
Published: over 4 years ago

10.3390/ijerph15030518

Erosion and Sediment Transport Modelling in Shallow Waters: A Review on Approaches, Models and Applications
Cited by: 59
Author(s): Mohammad Hajigholizadeh, Assefa M. Melesse, Héctor R. Fuentes
Software Mentions: 1
Published: over 6 years ago

10.3390/ijerph18168802

ArcDrain: A GIS Add-In for Automated Determination of Surface Runoff in Urban Catchments
Cited by: 3
Author(s): Cristina Manchado, Alejandro Roldán-Valcarce, Daniel Jato-Espino, Ignacio Andrés‐Domenech
Software Mentions: 1
Published: over 3 years ago

10.7554/eLife.45789

Transient protein accumulation at the center of the T cell antigen-presenting cell interface drives efficient IL-2 secretion
Cited by: 5
Author(s): Danielle J Clark, Laura E. McMillan, Sin Lih Tan, Gaia Bellomo, Clémentine Massoué, Harry Thompson, Lidiya Mykhaylechko, Dominic Alibhai, Xiongtao Ruan, Kentner L. Singleton, Minna Du, A. J. Hedges, Pamela L. Schwartzberg, Paul Verkade, Robert F. Murphy, Christoph Wülfing
Software Mentions: 1
Published: about 5 years ago

10.3390/ijms21186602

Comparison of High- and Low-LET Radiation-Induced DNA Double-Strand Break Processing in Living Cells
Cited by: 33
Author(s): Stefan J. Roobol, Irene van den Bent, Wiggert A. van Cappellen, Tsion E Abraham, Maarten W. Paul, Roland Kanaar, Adriaan B. Houtsmuller, Dik C. van Gent, Jeroen Essers
Software Mentions: 1
Published: about 4 years ago

10.1107/S0909049512044354

A comparative study of X-ray tomographic microscopy on shales at different synchrotron facilities: ALS, APS and SLS
Cited by: 46
Author(s): Waruntorn Kanitpanyacharoen, Dilworth Y. Parkinson, Francesco De Carlo, Federica Marone, Marco Stampanoni, Rajmund Mokso, Alastair A. MacDowell, H. R. Wenk
Software Mentions: 1
Published: almost 12 years ago

10.1080/21623945.2018.1521229

Proliferation of nutrition sensing preadipocytes upon short term HFD feeding
Cited by: 15
Author(s): Elisabeth Kulenkampff, Christian Wolfrum
Software Mentions: 1
Published: about 6 years ago

10.1111/jth.15171

Multimerin 1 supports platelet function in vivo and binds to specific GPAGPOGPX motifs in fibrillar collagens that enhance platelet adhesion
Cited by: 12
Author(s): Alexander Leatherdale, D'Andra Parker, Subia Tasneem, Yiming Wang, Dominique Bihan, Arkadiusz Bonna, Samir Hamaia, Peter L. Gross, Heyu Ni, Bradley W. Doble, David Lillicrap, Richard W. Farndale, Catherine P.M. Hayward
Software Mentions: 1
Published: almost 4 years ago

10.1007/s13280-016-0837-y

Land use influences macroinvertebrate community composition in boreal headwaters through altered stream conditions
Cited by: 27
Author(s): Micael Jonsson, Ryan M. Burrows, Johan Lidman, Emma Fältström, Hjalmar Laudon, Ryan A. Sponseller
Software Mentions: 1
Published: about 8 years ago

10.1186/1471-2105-14-294

Unsupervised segmentation of noisy electron microscopy images using salient watersheds and region merging
Cited by: 12
Author(s): Saket Navlakha, Parvez Ahammad, Eugene W. Myers
Software Mentions: 1
Published: about 11 years ago

10.1155/2016/5284586

Segmenting Brain Tissues from Chinese Visible Human Dataset by Deep-Learned Features with Stacked Autoencoder
Cited by: 7
Author(s): Guangjun Zhao, Xuchu Wang, Yanmin Niu, Liwen Tan, Shaoxiang Zhang
Software Mentions: 1
Published: almost 9 years ago

10.3390/biomedicines9070767

High Resolution Episcopic Microscopy for Qualitative and Quantitative Data in Phenotyping Altered Embryos and Adult Mice Using the New “Histo3D” System
Cited by: 6
Author(s): Wendling Olivia, Didier Hentsch, Hugues Jacobs, Nicolas Lemercier, Serge Taubert, Fabien Pertuy, Jean‐Luc Vonesch, Tania Sorg, Michela Di Michele, Laurent Le Cam, Thomas W. Rosahl, Ester Carballo-Jane, Mindy Liu, James Mu, Manuel Mark, Yann Hérault
Software Mentions: 1
Published: over 3 years ago

10.1007/s00429-019-01876-y

Connexin-36 distribution and layer-specific topography in the cat retina
Cited by: 5
Author(s): Ildikó Telkes, Péter Kóbor, József Orbán, Tamás Kovács-Öller, Béla Völgyi, Péter Buzás
Software Mentions: 1
Published: over 5 years ago

10.1039/c5lc01374g

Assessment of biocompatibility of 3D printed photopolymers using zebrafish embryo toxicity assays
Cited by: 135
Author(s): Niall P. Macdonald, Feng Zhu, Cathy W. Hall, Julien Reboud, Philip S. Crosier, E Elizabeth Patton, Donald Wlodkowic, Jonathan M. Cooper
Software Mentions: 1
Published: almost 9 years ago

10.1007/s10334-015-0521-4

A review of heart chamber segmentation for structural and functional analysis using cardiac magnetic resonance imaging
Cited by: 204
Author(s): Peng Peng, Karim Lekadir, Ali Gooya, Ling Shao, Steffen E. Petersen, Alejandro F. Frangi
Software Mentions: 1
Published: almost 9 years ago

10.3390/v11050390

Distinct Requirements for HIV-1 Accessory Proteins during Cell Coculture and Cell-Free Infection
Cited by: 9
Author(s): Anastasia Zotova, Anastasia Atemasova, Pichugin Alexey, Alexander Filatov, Dmitriy Mazurov
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pbio.1002340

Microscopy Image Browser: A Platform for Segmentation and Analysis of Multidimensional Datasets
Cited by: 285
Author(s): Ilya Belevich, Merja Joensuu, Darshan Kumar, Helena Vihinen, Eija Jokitalo
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0125825

A Context-Aware Delayed Agglomeration Framework for Electron Microscopy Segmentation
Cited by: 32
Author(s): Toufiq Parag, Anirban Chakraborty, Stephen M. Plaza, Louis K. Scheffer
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0190386

A novel expert system for objective masticatory efficiency assessment
Cited by: 9
Author(s): Gustavo Vaccaro, José Ignacio Peláez, José Antonio Gil-Montoya
Software Mentions: 1
Published: almost 7 years ago

10.1155/2013/430516

A Wavelet Relational Fuzzy<i>C</i>-Means Algorithm for 2D Gel Image Segmentation
Cited by: 1
Author(s): Shaheera Rashwan, Mohamed T. Faheem, Amany M. Sarhan, B Youssef
Software Mentions: 1
Published: almost 12 years ago

10.1186/1746-1596-9-92

Objective assessment of changes in nuclear morphology and cell distribution following induction of apoptosis
Cited by: 70
Author(s): Jon Roger Eidet, Lara Pasovic, Rima Maria, Catherine Jackson, Tor Paaske Utheim
Software Mentions: 1
Published: over 10 years ago

10.3389/fcell.2021.736574

A New Pipeline to Automatically Segment and Semi-Automatically Measure Bone Length on 3D Models Obtained by Computed Tomography
Cited by: 2
Author(s): Santiago Beltran Diaz, Chee Ho H’ng, Xinli Qu, Michael Doube, John Nguyen, Michael de Veer, Olga Panagiotopoulou, Alberto Roselló-Díez
Software Mentions: 1
Published: about 3 years ago

Projects: pypi: Watershed

Papers Mentioning Watershed 55