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List of works by Anne E Carpenter

2020 BioImage Analysis Survey: Community experiences and needs for the future

scientific article published in 2021

A Genome-wide RNAi Screen for Microtubule Bundle Formation and Lysosome Motility Regulation in Drosophila S2 Cells

scientific article published on 6 January 2016

A call for bioimaging software usability

scientific article published on 28 June 2012

A chemical screen probing the relationship between mitochondrial content and cell size

scientific article

A dataset of images and morphological profiles of 30,000 small-molecule treatments using the Cell Painting assay

scientific article

A field guide to cultivating computational biology

scientific article published on 08 October 2021

A microscale human liver platform that supports the hepatic stages of Plasmodium falciparum and vivax

scientific article published on July 2013

A novel small molecule regulator of guanine nucleotide exchange activity of the ADP-ribosylation factor and golgi membrane trafficking.

scientific article published on 17 September 2008

Abnormalities in mitochondrial structure in cells from patients with bipolar disorder

scientific article

Alteration of large-scale chromatin structure by estrogen receptor

scientific article

An image analysis toolbox for high-throughput C. elegans assays

scientific article

An intermittent live cell imaging screen for siRNA enhancers and suppressors of a kinesin-5 inhibitor

scientific article

An open-source computational tool to automatically quantify immunolabeled retinal ganglion cells

scientific article published on 24 April 2016

An open-source solution for advanced imaging flow cytometry data analysis using machine learning

scientific article

Annotated high-throughput microscopy image sets for validation ⬇️

scientific article published on June 28, 2012

Automated image-based assay for evaluation of HIV neutralization and cell-to-cell fusion inhibition

scientific article

Biological imaging software tools

scientific article published on 28 June 2012

CDy6, a photostable probe for long-term real-time visualization of mitosis and proliferating cells

scientific article

CP-CHARM: segmentation-free image classification made accessible

scientific article published on 27 January 2016

Capturing single-cell heterogeneity via data fusion improves image-based profiling

Capturing single-cell heterogeneity via data fusion improves image-based profiling

scientific article published on 07 May 2019

CellProfiler Analyst: data exploration and analysis software for complex image-based screens

scientific article

CellProfiler Tracer: exploring and validating high-throughput, time-lapse microscopy image data

scientific article

CellProfiler: free, versatile software for automated biological image analysis

scientific article published in January 2007

Comparison of methods for image-based profiling of cellular morphological responses to small-molecule treatment

scientific article

Data-analysis strategies for image-based cell profiling.

scientific article published on August 2017

Deductive automated pollen classification in environmental samples via exploratory deep learning and imaging flow cytometry

scientific article published in 2023

Deepometry, a framework for applying supervised and weakly supervised deep learning to imaging cytometry

scientific article published on 18 June 2021

Diagnostic Potential of Imaging Flow Cytometry.

scientific article published on 30 January 2018

Discovery of New Anti-Schistosomal Hits by Integration of QSAR-Based Virtual Screening and High Content Screening

scientific article

EXTRACTING BIOMEDICALLY IMPORTANT INFORMATION FROM LARGE, AUTOMATED IMAGING EXPERIMENTS.

scientific article published on January 2011

Erratum: Visualization of image data from cells to organisms

scholarly article by Thomas Walter et al published June 2010 in Nature Methods

Evaluation of Deep Learning Strategies for Nucleus Segmentation in Fluorescence Images

scholarly article published 31 May 2018

Evaluation of Deep Learning Strategies for Nucleus Segmentation in Fluorescence Images

scientific article published on 16 July 2019

Extracting rich information from images

scientific article

Genes in human obesity loci are causal obesity genes in C. elegans

scientific article published on 07 September 2021

Genome-scale RNAi on living-cell microarrays identifies novel regulators of Drosophila melanogaster TORC1-S6K pathway signaling

scientific article

Harnessing the power of microscopy images to accelerate drug discovery: what are the possibilities?

scientific article published on 21 March 2020

High content image analysis identifies novel regulators of synaptogenesis in a high-throughput RNAi screen of primary neurons

scientific article (publication date: 2014)

High- and low-throughput scoring of fat mass and body fat distribution in C. elegans.

scientific article

High-throughput screen for novel antimicrobials using a whole animal infection model

scientific article published on July 2009

High-throughput screens for fluorescent dye discovery

scientific article

Human tumors instigate granulin-expressing hematopoietic cells that promote malignancy by activating stromal fibroblasts in mice

scientific article

Identification and local delivery of vasodilators for the reduction of ureteral contractions

scientific article published on 02 December 2019

Identification of host-targeted small molecules that restrict intracellular Mycobacterium tuberculosis growth

scientific article (publication date: February 2014)

Image-based chemical screening

scientific article published on August 2007

Image-based profiling for drug discovery: due for a machine-learning upgrade?

scientific article published in 2020

Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software

scientific article

Increasing the Content of High-Content Screening: An Overview

scientific article

Introduction to the quantitative analysis of two-dimensional fluorescence microscopy images for cell-based screening

scientific article

Keras R-CNN: library for cell detection in biological images using deep neural networks

scientific article published on 11 July 2020

Label-Free Leukemia Monitoring by Computer Vision

scientific article published on 24 February 2020

Label-free cell cycle analysis for high-throughput imaging flow cytometry.

scientific article published on 7 January 2016

Mining for osteogenic surface topographies: In silico design to in vivo osseo-integration

scientific article published on 12 May 2017

Morphological Profiles of RNAi-Induced Gene Knockdown Are Highly Reproducible but Dominated by Seed Effects

scientific article published on 21 July 2015

Multiplex cytological profiling assay to measure diverse cellular states

scientific article (publication date: 2013)

Nanoparticle vesicle encoding for imaging and tracking cell populations ⬇️

scientific article

Niche-based screening identifies small-molecule inhibitors of leukemia stem cells

scientific article

Nucleus segmentation across imaging experiments: the 2018 Data Science Bowl

scientific article published on 21 October 2019

Objective assessment of stored blood quality by deep learning

scientific article published on 24 August 2020

Opportunities and obstacles for deep learning in biology and medicine.

scientific article published in April 2018

Pharmacological HIF2α inhibition improves VHL disease-associated phenotypes in zebrafish model

scientific article published on 13 April 2015

Pipeline for illumination correction of images for high-throughput microscopy

scientific article

Predicting drug polypharmacology from cell morphology readouts using variational autoencoder latent space arithmetic

scientific article published on 25 February 2022

ProtocolNavigator: emulation-based software for the design, documentation and reproduction biological experiments

scientific article

Publisher Correction: Nucleus segmentation across imaging experiments: the 2018 Data Science Bowl

scientific article published on 01 February 2020

PyImageJ: A library for integrating ImageJ and Python

scientific article published in 2022

Quality Control for High-Throughput Imaging Experiments Using Machine Learning in Cellprofiler.

scientific article published in January 2018

Quantifying co-cultured cell phenotypes in high-throughput using pixel-based classification

scientific article published on 11 December 2015

RESOLVING CLUSTERED WORMS VIA PROBABILISTIC SHAPE MODELS

scientific article published on June 2010

Reconstructing cell cycle and disease progression using deep learning

scientific article published on 6 September 2017

Scientific Community Image Forum: A discussion forum for scientific image software

scientific article published on 19 June 2019

Scoring diverse cellular morphologies in image-based screens with iterative feedback and machine learning

scientific article

Screening cellular feature measurements for image-based assay development

scientific article

Small molecules discovered in a pathway screen target the Rho pathway in cytokinesis

scientific article

Software opens the door to quantitative imaging

scientific article published on 01 February 2007

Systematic morphological profiling of human gene and allele function via Cell Painting.

scientific article published on 18 March 2017

Systematic, multiparametric analysis of Mycobacterium tuberculosis intracellular infection offers insight into coordinated virulence

scientific article

Toward performance-diverse small-molecule libraries for cell-based phenotypic screening using multiplexed high-dimensional profiling

scientific article

Ultrasome: efficient aberration caller for copy number studies of ultra-high resolution

scientific article published on 19 February 2009

Using CellProfiler for Automatic Identification and Measurement of Biological Objects in Images

scientific article (publication date: 5 January 2015)

Using CellProfiler for automatic identification and measurement of biological objects in images

scientific article

Visualization of Parameter Space for Image Analysis ⬇️

scientific article published on December 1, 2011

Weakly supervised learning of single-cell feature embeddings

Workflow and metrics for image quality control in large-scale high-content screens

scientific article published on 28 September 2011

ZFHX4 interacts with the NuRD core member CHD4 and regulates the glioblastoma tumor-initiating cell state

scientific journal article

mTOR complex 1 regulates lipin 1 localization to control the SREBP pathway

scientific article

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