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

Lee Kamentsky, Thouis R. Jones, Adam Fraser, Mark-Anthony Bray, David J. Logan, Katherine L. Madden, Vebjorn Ljosa, Curtis Rueden, Kevin W. Eliceiri, Anne E. Carpenter
2011 Computer applications in the biosciences : CABIOS  
There is a strong and growing need in the biology research community for accurate, automated image analysis.  ...  It is more robust and user friendly, with new algorithms and features to facilitate high-throughput work. ImageJ plugins can now be run within a CellProfiler pipeline.  ...  ACKNOWLEDGEMENTS The authors thank the members of their laboratories for contributing to the development of the software and this article, especially Shravas Rao and Emily Schloff.  ... 
doi:10.1093/bioinformatics/btr095 pmid:21349861 pmcid:PMC3072555 fatcat:syrv4mxysjh47c2aa6jky2s2di

CellProfiler: image analysis software for identifying and quantifying cell phenotypes

Anne E Carpenter, Thouis R Jones, Michael R Lamprecht, Colin Clarke, In Han Kang, Ola Friman, David A Guertin, Joo Han Chang, Robert A Lindquist, Jason Moffat, Polina Golland, David M Sabatini
2006 Genome Biology  
Here we describe the first free, open-source system designed for flexible, high-throughput cell image analysis, CellProfiler.  ...  Biologists can now prepare and image thousands of samples per day using automation, enabling chemical screens and functional genomics (for example, using RNA interference).  ...  to the software, Steve Lowe; and those who provided helpful comments, Doug Wheeler, Tamar Resnick and Kimberly Hartwell.  ... 
doi:10.1186/gb-2006-7-10-r100 pmid:17076895 pmcid:PMC1794559 fatcat:dyk4dzjftjactceynymom3h3pu

CellProfiler 3.0: Next-generation image processing for biology

Claire McQuin, Allen Goodman, Vasiliy Chernyshev, Lee Kamentsky, Beth A. Cimini, Kyle W. Karhohs, Minh Doan, Liya Ding, Susanne M. Rafelski, Derek Thirstrup, Winfried Wiegraebe, Shantanu Singh (+4 others)
2018 PLoS Biology  
CellProfiler has enabled the scientific research community to create flexible, modular image analysis pipelines since its release in 2005.  ...  Here, we describe CellProfiler 3.0, a new version of the software supporting both whole-volume and plane-wise analysis of three-dimensional (3D) image stacks, increasingly common in biomedical research  ...  Ulman and David Svoboda from Masaryk University for providing synthetic 3D images of HL60 cell line nuclei.  ... 
doi:10.1371/journal.pbio.2005970 pmid:29969450 pmcid:PMC6029841 fatcat:iozwv4nslnbl5n3s4ez2jz6qnu

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

Mark-Anthony Bray, Anne E. Carpenter
2015 BMC Bioinformatics  
Results: We present CellProfiler Tracer, a free and open-source tool that complements the object tracking functionality of the CellProfiler biological image analysis package.  ...  Time-lapse analysis of cellular images is an important and growing need in biology.  ...  Acknowledgments The authors thank the members of the Foe and Ramaswamy laboratories for contributing image data to the development of the software and this article, as well as John Albeck, Albert Yeh,  ... 
doi:10.1186/s12859-015-0759-x pmid:26537300 pmcid:PMC4634901 fatcat:b2fa6sarwnf2fnmsatyknhp36e

BRANE Cut: Biologically-Related A priori Network Enhancement with Graph cuts for Gene Regulatory Network Inference [article]

Aurélie Pirayre, Camille Couprie, Frédérique Bidard, Laurent Duval, Jean-Christophe Pesquet
2015 biorxiv/medrxiv   pre-print
We enforce biologically plausible coupling between groups and types of genes by minimizing an edge labeling functional coding for a priori structures.  ...  Inferring gene networks from high-throughput data constitutes an important step in the discovery of relevant regulatory relationships in organism cells.  ...  Acknowledgments The authors thank the members of the Foe and Ramaswamy laboratories for contributing image data to the development of the software and this article, as well as John Albeck, Albert Yeh,  ... 
doi:10.1101/032383 fatcat:2v44mu2janbwnapgjamecdgjuy

BRANE Cut: biologically-related a priori network enhancement with graph cuts for gene regulatory network inference

Aurélie Pirayre, Camille Couprie, Frédérique Bidard, Laurent Duval, Jean-Christophe Pesquet
2015 BMC Bioinformatics  
Results: We present CellProfiler Tracer, a free and open-source tool that complements the object tracking functionality of the CellProfiler biological image analysis package.  ...  Time-lapse analysis of cellular images is an important and growing need in biology.  ...  Acknowledgments The authors thank the members of the Foe and Ramaswamy laboratories for contributing image data to the development of the software and this article, as well as John Albeck, Albert Yeh,  ... 
doi:10.1186/s12859-015-0754-2 pmid:26537179 pmcid:PMC4634801 fatcat:nhufwyckvzglvcln5irzq2klju

Advanced Image Processing For Biology, And The Open Bio Image Alliance (Obia)

Ricard Delgado-Gonzalo, Daniel Sage, Michael Unser
2013 Zenodo  
Tracking cells and building lineage trees: The problem of tracking cells is central to high-throughput microscopy [3] .  ...  The use of modular structures with common interfaces allows developers to update their software with minimum effort.  ...  The topics are plentiful and challenging intellectually with a pressing need for better image processing and analysis tools.  ... 
doi:10.5281/zenodo.43577 fatcat:frtrtfpj3vfa5dgb4kbu4h56tu

CellSegm - a MATLAB toolbox for high-throughput 3D cell segmentation

Erlend Hodneland, Tanja Kögel, Dominik Frei, Hans-Hermann Gerdes, Arvid Lundervold
2013 Source Code for Biology and Medicine  
The modularity and scripting capabilities of CELLSEGM enable automated workflows and quantitative analysis of microscopic data, suited for high-throughput image based screening.  ...  Automated cell segmentation is useful for the analysis of cells imaged by fluorescence microscopy, both in terms of objectivity and reduced work load.  ...  The stained and embedded skin biopsy was a generous gift from Ole Johnny Steffensen, Department of pathology, Ålesund Hospital, Ålesund, Norway.The confocal imaging was  ... 
doi:10.1186/1751-0473-8-16 pmid:23938087 pmcid:PMC3850890 fatcat:kqoi5fjgifdbdnq7ncjvf4c52u

IA-Lab: A MATLAB framework for efficient microscopy image analysis development, applied to quantifying intracellular transport of internalized peptide-drug conjugate

Adam M. Corrigan, Johan Karlsson, Jan Wildenhain, Laurent Knerr, Maria Ölwegård-Halvarsson, Maria Karlsson, Svenja Lünse, Yinhai Wang, Vadim E. Degtyar
2019 PLoS ONE  
This work presents a MATLAB-based software package for high-throughput microscopy image analysis development, making such development more accessible for a large user community.  ...  The toolbox provides a GUI and a number of analysis workflows, and can serve as a general framework designed to allow for easy extension.  ...  Introduction High-throughput microscopy image analysis is an area of increasing importance for biomedical research in academia and the pharmaceutical industry, with experiments and subsequent image analytics  ... 
doi:10.1371/journal.pone.0220627 pmid:31369634 pmcid:PMC6675096 fatcat:vygl4bvifrhs5a3pzw6c2pb2mu

Biological imaging software tools

Kevin W Eliceiri, Michael R Berthold, Ilya G Goldberg, Luis Ibáñez, B S Manjunath, Maryann E Martone, Robert F Murphy, Hanchuan Peng, Anne L Plant, Badrinath Roysam, Nico Stuurman, Jason R Swedlow (+2 others)
2012 Nature Methods  
Narayanswamy of the Roysam lab for their assistance in preparing figures, and L. Kamentsky and M. Bray of the Carpenter lab for useful input and edits on the manuscript.  ...  ACKNOwLEdGMENTS We acknowledge our respective funding sources and members of our laboratories for feedback and useful comments, in particular A. Merouane and A.  ...  Imaging and High-Throughput Phenotyping meeting.  ... 
doi:10.1038/nmeth.2084 pmid:22743775 pmcid:PMC3659807 fatcat:6wnzuhdrdfd67o72cmcgwwpgka

Supplementary Material for: Differential Neuroprotective Effects of Interleukin-1 Receptor Antagonist on Spinal Cord Neurons after Excitotoxic Injury

N. Schizas, S. Perry, B. Andersson, C. Wählby, K. Kullander, N.P. Hailer
2018 Figshare  
Immunohistochemistry for neuronal nuclei (NeuN), MacII, glial fibrillary acidic protein, and TdT-mediated dUTP nick end labelling stains were used to evaluate neuronal survival, glial activation, and apoptosis  ...  We hypothesized that the interleukin-1 receptor antagonist (IL1RA) protects neuronal populations and suppresses apoptosis and gliosis after injury.  ...  Kamentsky L, Jones TR, Fraser A, Bray M, Logan D, Madden K, Ljosa V, Rueden C, Harris GB, Eliceiri K, Carpenter AE (2011) Improved structure, function, and compatibility for CellProfiler: modular high-throughput  ... 
doi:10.6084/m9.figshare.5821617.v1 fatcat:6gyaufj6u5bx7p477tf7vg5pqu

Image Analysis of the Mitochondrial Network Morphology With Applications in Cancer Research

Ching-Hsiang Chu, Wen-Wei Tseng, Chan-Min Hsu, An-Chi Wei
2022 Frontiers in Physics  
We listed and applied pipelines and packages available in ImageJ/Fiji, CellProfiler, MATLAB, Java, and Python for the analysis of fluorescently labeled mitochondria in microscopy images and compared their  ...  We reviewed the current image-based analytical tools and machine-learning techniques for phenotyping mitochondrial morphology in different cancer cell lines from confocal microscopy images.  ...  Improved Structure, Function and Compatibility for CellProfiler: Modular High-Throughput Image Analysis Software.  ... 
doi:10.3389/fphy.2022.855775 doaj:5498f680cd72461d9fdc7b8f0d4a23f8 fatcat:g76u6idpffeclnfkj7odhkf6p4

Introduction to the Quantitative Analysis of Two-Dimensional Fluorescence Microscopy Images for Cell-Based Screening

Vebjorn Ljosa, Anne E. Carpenter, Fran Lewitter
2009 PLoS Computational Biology  
High-throughput microscope vendors often bundle some data-analysis functionality with their instruments and imageanalysis software.  ...  High-throughput screening software and general tools for multivariate analysis and visualization (e.g., GeneData Screener, SciTegic Pipeline Pilot, and SpotFire) have proven useful for imagebased measurements  ... 
doi:10.1371/journal.pcbi.1000603 pmid:20041172 pmcid:PMC2791844 fatcat:hsc3roxljbbqndxtu2fmouuah4

Ultrahigh-throughput generation and characterization of cellular aggregates in laser-ablated microwells of poly(dimethylsiloxane)

Jacob L. Albritton, Jonathon D. Roybal, Samantha J. Paulsen, Nicholas J. Calafat, Jose A. Flores-Zaher, Mary C. Farach-Carson, Don L. Gibbons, Jordan S. Miller
2016 RSC Advances  
We modified a CO2 laser cutter to rapidly ablate PDMS and form conical microwells with customizable dimensions, which can serve to easily aggregate cells into uniform shapes in ultrahigh-throughput supply  ...  Tim Schmidt for his help with adapting Marlin firmware to our laser cutter and Mr.  ...  Sederstrom and the Cytometry and Cell Sorting Core at Baylor College of Medicine for assistance with cell sorting.  ... 
doi:10.1039/c5ra26022a pmid:26998251 pmcid:PMC4792302 fatcat:i3uimvbi6rcrpjopqm4dnetloe

Automated hiPSC culture and sample preparation for 3D live cell microscopy [article]

Mackenzie E. Coston, Benjamin W. Gregor, Joy Arakaki, Antoine Borensztejn, Thao P. Do, Margaret A. Fuqua, Amanda Haupt, Melissa C. Hendershott, Winnie Leung, Irina A. Mueller, Angelique M. Nelson, Susanne M. Rafelski (+7 others)
2020 bioRxiv   pre-print
Additionally, we developed an automated image-based colony segmentation and feature extraction pipeline to predict cell count and select wells with consistent morphology for high resolution 3D microscopy  ...  To do this, we image human inducible pluripotent stem cell (hiPSC) lines expressing fluorescently tagged protein representing specific cellular organelles and structures.  ...  Acknowledgements We thank Jenny Burn for editing the video tutorial, Alan R. Horwitz and the Allen Institute for Cell Science Team for helpful discussions.  ... 
doi:10.1101/2020.12.18.423371 fatcat:gvaxvt5ervc3dlf7vs34tnud4m
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