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SCIFIO: an extensible framework to support scientific image formats

Mark C. Hiner, Curtis T. Rueden, Kevin W. Eliceiri
2016 BMC Bioinformatics  
SCIFIO is structured to support coexistence of multiple domain-specific open exchange formats, such as Bio-Formats' OME-TIFF, within a unified environment.  ...  Conclusions: SCIFIO is a freely available software library developed to standardize the process of reading and writing scientific image formats.  ...  Acknowledgements Many people have contributed to the development of SCIFIO on both technical and leadership levels.  ... 
doi:10.1186/s12859-016-1383-0 pmid:27927161 pmcid:PMC5142403 fatcat:h426vct23fbo3iroqffmn3yome

ImageJ2: ImageJ for the next generation of scientific image data

Curtis T. Rueden, Johannes Schindelin, Mark C. Hiner, Barry E. DeZonia, Alison E. Walter, Ellen T. Arena, Kevin W. Eliceiri
2017 BMC Bioinformatics  
ImageJ is an image analysis program extensively used in the biological sciences and beyond.  ...  Its robust new plugin framework allows everything from image formats, to scripting languages, to visualization to be extended by the community.  ...  Further details about SCIFIO can be found in the BioMed Central (BMC) Bioinformatics software article "SCIFIO: an extensible framework to support scientific image formats" [28] .  ... 
doi:10.1186/s12859-017-1934-z pmid:29187165 pmcid:PMC5708080 fatcat:micm7kue5jcxjk372tagjgskuu

ImageJ2: ImageJ for the next generation of scientific image data [article]

Curtis T. Rueden, Johannes Schindelin, Mark C. Hiner, Barry E. DeZonia, Alison E. Walter, Ellen T. Arena, Kevin W. Eliceiri
2017 arXiv   pre-print
ImageJ is an image analysis program extensively used in the biological sciences and beyond.  ...  Its robust new plugin framework allows everything from image formats, to scripting languages, to visualization to be extended by the community.  ...  Finally, our deep thanks to the NIH, whose initial funding of ImageJ2 in 2009 was instrumental in launching the project, as well as to all funding agencies and organizations who have supported the project's  ... 
arXiv:1701.05940v4 fatcat:4ttvwx5dh5e4vjmcd3gmy33ohe

Bioinformatics Solutions for Image Data Processing [chapter]

Pietro Cinaglia, Luciano Caroprese, Giuseppe Lucio Cascini, Francesco Dattola, Pasquale Iaquinta, Miriam Iusi, Pierangelo Veltri, Ester Zumpano
2018 Medical and Biological Image Analysis  
solutions and toolkits for medical imaging in order to suggest an overview of techniques and methods that can be applied for the imaging analysis in medicine.  ...  Bioinformatics solutions provide an effective approach for image data processing in order to retrieve information of interest and to integrate several data sources for knowledge extraction; furthermore  ...  In other words, it is a library for reading and writing N-dimensional image data. SCIFIO is an open source plugin for the SciJava framework that offers support for handling of scientific images.  ... 
doi:10.5772/intechopen.76459 fatcat:kejwf2t3rrcjnccmad4d2jskwa

The ImageJ ecosystem: An open platform for biomedical image analysis

Johannes Schindelin, Curtis T. Rueden, Mark C. Hiner, Kevin W. Eliceiri
2015 Molecular Reproduction and Development  
The software's extensibility continues to attract biologists at all career stages as well as computer scientists who wish to effectively implement specific image-processing algorithms.  ...  In this review, we use the ImageJ project as a case study of how open-source software fosters its suites of software tools, making multitudes of image-analysis technology easily accessible to the scientific  ...  ACKNOWLEDGMENTS The authors would like to thank Stephan Saalfeld for the CLAHE example image; Ignacio Arganda-Carreras for the trainable segmentation example image; Stephan Preibisch for the stitching  ... 
doi:10.1002/mrd.22489 pmid:26153368 pmcid:PMC5428984 fatcat:lxho2lvzqvevvfj4rmnprhlvjm

BoneJ2 - refactoring established research software

Richard Domander, Alessandro A Felder, Michael Doube
2021 Wellcome Open Research  
We reimplemented BoneJ, our software for skeletal biology image analysis, to address design limitations that put it at risk of becoming unusable.  ...  While such code can help find answers to specific research questions, it may lack longevity and flexibility to make it reusable.  ...  We added the plugins that read custom file formats to SCIFIO (SCientific Image Format Input and Output), so now ImageJ can open them without users needing to install BoneJ.  ... 
doi:10.12688/wellcomeopenres.16619.1 pmid:33954267 pmcid:PMC8063517 fatcat:rdfmzobyrrfzfjo23t37wflgna

BoneJ2 - refactoring established research software [version 2; peer review: 3 approved]

Richard Domander, Alessandro A Felder, Michael Doube
2021 Wellcome Open Research  
We reimplemented BoneJ, our software for skeletal biology image analysis, to address design limitations that put it at risk of becoming unusable.  ...  While such code can help find answers to specific research questions, it may lack longevity and flexibility to make it reusable.  ...  We added the plugins that read custom file formats to SCIFIO (SCientific Image Format Input and Output), so now ImageJ can open them without users needing to install BoneJ.  ... 
doi:10.12688/wellcomeopenres.16619.2 doaj:d1a3f18733cc4c22869a43bda793dafb fatcat:hvbv242p2fgupoewdmbsl5o7w4

Integration of the ImageJ Ecosystem in KNIME Analytics Platform

Christian Dietz, Curtis T. Rueden, Stefan Helfrich, Ellen T. A. Dobson, Martin Horn, Jan Eglinger, Edward L. Evans, Dalton T. McLean, Tatiana Novitskaya, William A. Ricke, Nathan M. Sherer, Andries Zijlstra (+2 others)
2020 Frontiers in Computer Science  
Scientists are often forced to create highly specialized and hard-to-reproduce scripts to orchestrate individual software fragments and cover the entire life-cycle of an analysis of an image dataset.  ...  Here we present how users and developers alike can leverage the ImageJ ecosystem via the KNIME Image Processing extension to provide robust and extensible image analysis within KNIME workflows.  ...  For biological use case no. 1, we thank Katie Hebron for providing the images.  ... 
doi:10.3389/fcomp.2020.00008 pmid:32905440 pmcid:PMC7469687 fatcat:swuw4yfkpbd4hoplfbybs5beji

FLIMJ: an open-source ImageJ toolkit for fluorescence lifetime image data analysis [article]

Dasong W Gao, Paul R Barber, Jenu V Chacko, Abdul Kader Sagar, Curtis T Rueden, Aivar R Grislis, Mark Hiner, Kevin W. Eliceiri
2020 bioRxiv   pre-print
To address this need, we have created FLIMJ, an ImageJ plugin and toolkit that allows for easy use and development of extensible image analysis workflows with FLIM data.  ...  Built on the FLIMLib decay curve fitting library and the ImageJ Ops framework, FLIMJ offers FLIM fitting routines with seamless integration with other ImageJ components, and the ability to be extended  ...  supported through the use of the SCIFIO (http://scif.io/) infrastructures (23) to support a range of open and proprietary FLIM file formats.  ... 
doi:10.1101/2020.08.17.253625 fatcat:ajsbosh6pnafzontybejndq7gu

FLIMJ: An open-source ImageJ toolkit for fluorescence lifetime image data analysis

Dasong Gao, Paul R. Barber, Jenu V. Chacko, Md. Abdul Kader Sagar, Curtis T. Rueden, Aivar R. Grislis, Mark C. Hiner, Kevin W. Eliceiri, Kristen C. Maitland
2020 PLoS ONE  
To address this need, we have created FLIMJ, an ImageJ plugin and toolkit that allows for easy use and development of extensible image analysis workflows with FLIM data.  ...  We show the extensibility of FLIMJ in two analysis scenarios: lifetime-based image segmentation and image colocalization.  ...  Gilbey for their significant contributions to the development of the original algorithms in TRI2, J. Nedbal for the MATLAB wrapper to FLIMlib and M. Rowley and T.  ... 
doi:10.1371/journal.pone.0238327 pmid:33378370 fatcat:elbj4bpqqvcndeljmxyp5czr2a

Mars, a molecule archive suite for reproducible analysis and reporting of single molecule properties from bioimages [article]

Nadia M Huisjes, Thomas M Retzer, Matthias J Scherr, Rohit Agarwal, Barbara Safaric, Anita Minnen, Karl E Duderstadt
2021 bioRxiv   pre-print
Mars provides a flexible solution for reproducible analysis of image-derived properties facilitating the discovery and quantitative classification of new biological phenomena with an open data format accessible  ...  Here, we present Mars, an open-source platform for storage and processing of image-derived properties of biomolecules.  ...  We are grateful to Giovanni Cardone (MPIB imaging facility) and Evelyn Plötz for their helpful feedback on the project. We would like to thank Prof.  ... 
doi:10.1101/2021.11.26.470105 fatcat:bohrhmp3lnfwpipyfr4nefqkwi

Is the Stack Distance Between Test Case and Method Correlated With Test Effectiveness?

Rainer Niedermayr, Stefan Wagner
2019 Proceedings of the Evaluation and Assessment on Software Engineering - EASE '19  
We conducted an empirical study with 21 open-source projects, which comprise in total 1.8 million LOC, and show that a correlation exists between stack distance and test effectiveness.  ...  The correlation reaches a strength up to 0.58.  ...  For that, we used Pitest (PIT) [10] in version 1.4.0 with the pit-mp extension to support multi-module projects.  ... 
doi:10.1145/3319008.3319021 dblp:conf/ease/Niedermayr019 fatcat:ih37kpeuvbcxfbb2xj2l2zdrgu

A comprehensive study of pseudo-tested methods

Oscar Luis Vera-Pérez, Benjamin Danglot, Martin Monperrus, Benoit Baudry
2018 Empirical Software Engineering  
Second, we perform a systematic characterization of these methods, both quantitatively and qualitatively with an extensive manual analysis of 101 pseudo-tested methods.  ...  not pay the testing price to fix this situation.  ...  This work has been partially supported by the EU Project STAMP ICT-16-10 No.731529 and by the Wallenberg Autonomous Systems and Software Program (WASP) funded by the Knut and Alice Wallenberg Foundation  ... 
doi:10.1007/s10664-018-9653-2 fatcat:dydyrdlt4fcl7g2tq36jpbbhla

ITK: enabling reproducible research and open science

Matthew McCormick, Xiaoxiao Liu, Julien Jomier, Charles Marion, Luis Ibanez
2014 Frontiers in Neuroinformatics  
ACKNOWLEDGMENTS We would like to thank the Insight Toolkit community, which we are honored to participant in. We would like to thank Dr.  ...  Technology Support of the NLM's Insight Toolkit (ITK-v4)" contract number HHSN276201300003I.  ...  Arbitrary pixel types are supported, and a number of standard and medical imaging specific file formats for 2D, 3D, and ND datasets are supported, including BioRad, BMP, CSV, DICOM via the GDCM or DCMTK  ... 
doi:10.3389/fninf.2014.00013 pmid:24600387 pmcid:PMC3929840 fatcat:j3igmstkr5gz7ama67sv4wduum

Hidden Markov model and Chapman Kolmogrov for protein structures prediction from images

Md. Sarwar Kamal, Linkon Chowdhury, Mohammad Ibrahim Khan, Amira S. Ashour, João Manuel R.S. Tavares, Nilanjan Dey
2017 Computational biology and chemistry  
Initially, a preprocessing stage was applied for protein images' binarization using Otsu technique in order to convert the protein image into binary matrix.  ...  The current work proposed a protein prediction approach from protein images based on Hidden Markov Model and Chapman Kolmogrov equation.  ...  SCIFIO (SCientific Image Format Input and Output) is a library that a Bio-Formats to create a domain-independent image I/O framework [78] .The goal of SCIFIO is to integrate the scientific formats between  ... 
doi:10.1016/j.compbiolchem.2017.04.003 pmid:28432981 fatcat:t5alpi5xjngfjkbl7dr2z6zfvi
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