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3 changes: 3 additions & 0 deletions _sources/blog/readme.md
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[https://focalplane.biologists.com/2023/07/26/sharing-your-poster-on-figshare/](https://focalplane.biologists.com/2023/07/26/sharing-your-poster-on-figshare/)

## Running Deep-Learning Scripts in the BiA-PoL Omero Server
By Marcelo Zoccoler



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[https://biapol.github.io/blog/robert_haase/browsing_idr/readme.html](https://biapol.github.io/blog/robert_haase/browsing_idr/readme.html)

## Getting started with Mambaforge and Python
By Mara Lampert



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[https://datamanagement.hms.harvard.edu/news/promoting-data-management-nikon-imaging-center-and-cell-biology-microscopy-facility](https://datamanagement.hms.harvard.edu/news/promoting-data-management-nikon-imaging-center-and-cell-biology-microscopy-facility)

## Data handling in large-scale electron microscopy
By Job Fermie



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3 changes: 3 additions & 0 deletions _sources/collection/readme.md
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[https://github.com/zeissmicroscopy/ZEN_Python_OAD_workshop](https://github.com/zeissmicroscopy/ZEN_Python_OAD_workshop)

## Research Data Management Seminar - Slides
By Della Chiesa, Stefano



[https://zenodo.org/record/6602101](https://zenodo.org/record/6602101)

## A biologist’s guide to planning and performing quantitative bioimaging experiments
By Rebecca A. Senft ,Barbara Diaz-Rohrer ,Pina Colarusso,Lucy Swift,Nasim Jamali,Helena Jambor,Thomas Pengo,Craig Brideau,Paula Montero Llopis,Virginie Uhlmann,Jason Kirk,Kevin Andrew Gonzales,Peter Bankhead,Edward L. Evans III,Kevin W. Eliceiri,Beth A. Cimini



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[https://www.bioimagingguide.org/](https://www.bioimagingguide.org/)

## Annotated high-throughput microscopy image sets for validation
By Vebjorn Ljosa, Katherine L Sokolnicki, Anne E Carpenter



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# document
## BiaPy: Bioimage analysis pipelines in Python
By Daniel Franco-Barranco et al



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4 changes: 4 additions & 0 deletions _sources/documentation/readme.md
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# documentation
## JIPipe: visual batch processing for ImageJ
By Ruman Gerst, Zoltán Cseresnyés & Marc Thilo Figge



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[https://jipipe.hki-jena.de/](https://jipipe.hki-jena.de/)

## MiToBo - A Toolbox for Image Processing and Analysis
By Birgit Möller, Markus Glaß, Danny Misiak, Stefan Posch



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[https://mitobo.informatik.uni-halle.de/](https://mitobo.informatik.uni-halle.de/)

## BiaPy: Bioimage analysis pipelines in Python
By Daniel Franco-Barranco et al



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[https://academic.oup.com/bioinformatics/article/28/19/2520/290322](https://academic.oup.com/bioinformatics/article/28/19/2520/290322)

## ModularImageAnalysis (MIA): Assembly of modularisedimage and object analysis workflows in ImageJ
By Stephen J. Cross, Jordan D. J. R. Fisher, Mark A. Jepson



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29 changes: 29 additions & 0 deletions _sources/publication/readme.md
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# publication
## MethodsJ2: a software tool to capture metadata and generate comprehensive microscopy methods text
By Joel Ryan, Thomas Pengo, Alex Rigano, Paula Montero Llopis, Michelle S. Itano, Lisa A. Cameron, Guillermo Marqués, Caterina Strambio-De-Castillia, Mark A. Sanders, Claire M. Brown



[https://www.nature.com/articles/s41592-021-01290-5](https://www.nature.com/articles/s41592-021-01290-5)

## Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications
By Alessandro Rigano et al.



[https://doi.org/10.1038/s41592-021-01315-z](https://doi.org/10.1038/s41592-021-01315-z)

## Metadata matters: access to image data in the real world
By Melissa Linkert et al.
Published 2010


[https://rupress.org/jcb/article/189/5/777/35828/Metadata-matters-access-to-image-data-in-the-real](https://rupress.org/jcb/article/189/5/777/35828/Metadata-matters-access-to-image-data-in-the-real)

## A call for public archives for biological image data
By Jan Ellenberg, Jason R. Swedlow, Mary Barlow, Charles E. Cook, Ugis Sarkans, Ardan Patwardhan, Alvis Brazma, Ewan Birney



[https://www.nature.com/articles/s41592-018-0195-8](https://www.nature.com/articles/s41592-018-0195-8)

## 2020 BioImage Analysis Survey: Community experiences and needs for the future
By Nasim Jamali, Ellen T. A. Dobson, Kevin W. Eliceiri, Anne E. Carpenter, Beth A. Cimini
Published 2021


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[https://github.com/ciminilab/2021_Jamali_BiologicalImaging](https://github.com/ciminilab/2021_Jamali_BiologicalImaging)

## Bridging Imaging Users to Imaging Analysis - A community survey
By Suganya Sivagurunathan, Stefania Marcotti, Carl J Nelson, Martin L Jones, David J Barry, Thomas J A Slater, Kevin W Eliceiri, Beth A Cimini
Published 2023


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[https://github.com/COBA-NIH/2023_ImageAnalysisSurvey](https://github.com/COBA-NIH/2023_ImageAnalysisSurvey)

## Understanding metric-related pitfalls in image analysis validation
By Annika Reinke et al
Published 2023


Expand All @@ -48,18 +55,21 @@ This article gives a detailed overview about pitfalls when using metric for imag
[https://arxiv.org/abs/2302.01790v3](https://arxiv.org/abs/2302.01790v3)

## Building a FAIR image data ecosystem for microscopy communities
By Isabel Kemmer, Antje Keppler, Beatriz Serrano-Solano, Arina Rybina, Buğra Özdemir, Johanna Bischof, Ayoub El Ghadraoui, John E. Eriksson, Aastha Mathur



[https://link.springer.com/article/10.1007/s00418-023-02203-7](https://link.springer.com/article/10.1007/s00418-023-02203-7)

## A study on long-term reproducibility of image analysis results on ImageJ and Fiji
By Robert Haase, Deborah Schmidt, Wayne Rasband, Curtis Rueden, Florian Jug, Pavel Tomancak, Eugene W. Myers



[https://figshare.com/articles/poster/I2K_Poster_Haase_V6_ImageJ_repro_pdf/7409525](https://figshare.com/articles/poster/I2K_Poster_Haase_V6_ImageJ_repro_pdf/7409525)

## JIPipe: visual batch processing for ImageJ
By Ruman Gerst, Zoltán Cseresnyés & Marc Thilo Figge



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[https://jipipe.hki-jena.de/](https://jipipe.hki-jena.de/)

## MiToBo - A Toolbox for Image Processing and Analysis
By Birgit Möller, Markus Glaß, Danny Misiak, Stefan Posch



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[https://mitobo.informatik.uni-halle.de/](https://mitobo.informatik.uni-halle.de/)

## ModularImageAnalysis (MIA): Assembly of modularisedimage and object analysis workflows in ImageJ
By Stephen J. Cross, Jordan D. J. R. Fisher, Mark A. Jepson



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[https://doi.org/10.52825/cordi.v1i.285](https://doi.org/10.52825/cordi.v1i.285)

## The Fiji Updater
By Robert Haase



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[https://analyticalscience.wiley.com/do/10.1002/was.0004000112/](https://analyticalscience.wiley.com/do/10.1002/was.0004000112/)

## CLIJ: GPU-accelerated image processing for everyone
By Robert Haase, Loic Royer, et al
Published 2020


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[https://doi.org/10.1038/s41592-019-0650-1](https://doi.org/10.1038/s41592-019-0650-1)

## A Hitchhiker's guide through the bio-image analysis software universe
By Robert Haase, Elnaz Fazeli, David Legland, Michael Doube, Siân Culley, Ilya Belevich, Eija Jokitalo, Martin Schorb, Anna Klemm, Christian Tischer



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[https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14451](https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14451)

## Challenges and opportunities for bioimage analysis core-facilities
By Johannes Richard Soltwedel, Robert Haase



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[https://onlinelibrary.wiley.com/doi/full/10.1111/jmi.13192](https://onlinelibrary.wiley.com/doi/full/10.1111/jmi.13192)

## Open microscopy in the life sciences: quo vadis?
By Johannes Hohlbein, Benedict Diederich, Barbora Marsikova, Emmanuel G. Reynaud, Séamus Holden, Wiebke Jahr, Robert Haase, Kirti Prakash
Published 2022


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[https://doi.org/10.1038/s41592-022-01602-3](https://doi.org/10.1038/s41592-022-01602-3)

## Developing open-source software for bioimage analysis: opportunities and challenges
By Florian Levet, Anne E. Carpenter, Kevin W. Eliceiri, Anna Kreshuk, Peter Bankhead, Robert Haase



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[https://f1000research.com/articles/10-302](https://f1000research.com/articles/10-302)

## Meeting in the Middle: Towards Successful Multidisciplinary Bioimage Analysis Collaboration
By Anjalie Schlaeppi, Wilson Adams, Robert Haase, Jan Huisken, Ryan B. MacDonald, Kevin W. Eliceiri, Elisabeth C. Kugler



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[https://www.frontiersin.org/articles/10.3389/fbinf.2022.889755/full](https://www.frontiersin.org/articles/10.3389/fbinf.2022.889755/full)

## Highlights from the 2016-2020 NEUBIAS training schools for Bioimage Analysts: a success story and key asset for analysts and life scientists
By Gabriel G. Martins, Fabrice P. Cordelières, Julien Colombelli, Rocco D’Antuono, Ofra Golani, Romain Guiet, Robert Haase, Anna H. Klemm, Marion Louveaux, Perrine Paul-Gilloteaux, Jean-Yves Tinevez, Kota Miura
Published 2021


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[https://f1000research.com/articles/10-334/v1](https://f1000research.com/articles/10-334/v1)

## REMBI: Recommended Metadata for Biological Images—enabling reuse of microscopy data in biology
By Ugis Sarkans et al



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[https://www.nature.com/articles/s41592-021-01166-8](https://www.nature.com/articles/s41592-021-01166-8)

## MDEmic: a metadata annotation tool to facilitate management of FAIR image data in the bioimaging community
By Susanne Kunis, Sebastian Hänsch, Christian Schmidt, Frances Wong, Caterina Strambio-De-Castillia, Stefanie Weidtkamp-Peters



Expand All @@ -235,6 +257,7 @@ Tags: NFDI4BioImage
[https://www.nature.com/articles/s41592-021-01288-z](https://www.nature.com/articles/s41592-021-01288-z)

## QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy
By Glyn Nelson, Ulrike Boehme, et al



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[https://www.nature.com/articles/s41592-021-01326-w](https://www.nature.com/articles/s41592-021-01326-w)

## NFDI4BIOIMAGE: Perspective for a national bioimaging standard
By Josh Moore, Susanne Kunis



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[https://ceur-ws.org/Vol-3415/paper-27.pdf](https://ceur-ws.org/Vol-3415/paper-27.pdf)

## SpatialData: an open and universal data framework for spatial omics
By Luca Marconato, Giovanni Palla, Kevin A Yamauchi, Isaac Virshup, Elyas Heidari, Tim Treis, Marcella Toth, Rahul Shrestha, Harald Vöhringer, Wolfgang Huber, Moritz Gerstung, Josh Moore, Fabian J Theis, Oliver Stegle



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[https://www.biorxiv.org/content/10.1101/2023.05.05.539647v1.abstract](https://www.biorxiv.org/content/10.1101/2023.05.05.539647v1.abstract)

## Community-developed checklists for publishing images and image analyses
By Christopher Schmied, Michael S Nelson, Sergiy Avilov, Gert-Jan Bakker, Cristina Bertocchi, Johanna Bischof, Ulrike Boehm, Jan Brocher, Mariana T Carvalho, Catalin Chiritescu, Jana Christopher, Beth A Cimini, Eduardo Conde-Sousa, Michael Ebner, Rupert Ecker, Kevin Eliceiri, Julia Fernandez-Rodriguez, Nathalie Gaudreault, Laurent Gelman, David Grunwald, Tingting Gu, Nadia Halidi, Mathias Hammer, Matthew Hartley, Marie Held, Florian Jug, Varun Kapoor, Ayse Aslihan Koksoy, Judith Lacoste, Sylvia Le Dévédec, Sylvie Le Guyader, Penghuan Liu, Gabriel G Martins, Aastha Mathur, Kota Miura, Paula Montero Llopis, Roland Nitschke, Alison North, Adam C Parslow, Alex Payne-Dwyer, Laure Plantard, Rizwan Ali, Britta Schroth-Diez, Lucas Schütz, Ryan T Scott, Arne Seitz, Olaf Selchow, Ved P Sharma, Martin Spitaler, Sathya Srinivasan, Caterina Strambio-De-Castillia, Douglas Taatjes, Christian Tischer, Helena Klara Jambor



Expand All @@ -276,6 +302,7 @@ Tags: NFDI4BioImage
[https://www.nature.com/articles/s41592-023-01987-9](https://www.nature.com/articles/s41592-023-01987-9)

## BigDataProcessor2: A free and open-source Fiji plugin for inspection and processing of TB sized image data
By Christian Tischer, Ashis Ravindran, Sabine Reither, Nicolas Chiaruttini, Rainer Pepperkok, Nils Norlin



Expand All @@ -284,6 +311,7 @@ Tags: NFDI4BioImage
[https://doi.org/10.1093/bioinformatics/btab106](https://doi.org/10.1093/bioinformatics/btab106)

## EDAM-bioimaging: The ontology of bioimage informatics operations, topics, data, and formats (update 2020)
By Matúš Kalaš, Laure Plantard, Joakim Lindblad, Martin Jones, Nataša Sladoje, Moritz A Kirschmann, Anatole Chessel, Leandro Scholz, Fabianne Rössler, Laura Nicolás Sáenz, Estibaliz Gómez de Mariscal, John Bogovic, Alexandre Dufour, Xavier Heiligenstein, Dominic Waithe, Marie-Charlotte Domart, Matthia Karreman, Raf Van de Plas, Robert Haase, David Hörl, Lassi Paavolainen, Ivana Vrhovac Madunić, Dean Karaica, Arrate Muñoz-Barrutia, Paula Sampaio, Daniel Sage, Sebastian Munck, Ofra Golani, Josh Moore, Florian Levet, Jon Ison, Alban Gaignard, Hervé Ménager, Chong Zhang, Kota Miura, Julien Colombelli, Perrine Paul-Gilloteaux



Expand All @@ -292,6 +320,7 @@ Tags: NFDI4BioImage
[https://f1000research.com/posters/9-162](https://f1000research.com/posters/9-162)

## A biologist’s guide to planning and performing quantitative bioimaging experiments
By Rebecca A. Senft ,Barbara Diaz-Rohrer ,Pina Colarusso,Lucy Swift,Nasim Jamali,Helena Jambor,Thomas Pengo,Craig Brideau,Paula Montero Llopis,Virginie Uhlmann,Jason Kirk,Kevin Andrew Gonzales,Peter Bankhead,Edward L. Evans III,Kevin W. Eliceiri,Beth A. Cimini



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# NFDI4BioImage Training Materials

This Jupyter Book contains 108 links to training materials in the context Research Data Management for Bioimaging / Microscopy Data and Bio-image Analysis and has been updated 2023-10-10.
This Jupyter Book contains 108 links to training materials in the context Research Data Management for Bioimaging / Microscopy Data and Bio-image Analysis and has been updated 2023-10-13.

This is a **preliminary** / **experimental** search index allowing us to explore how such a database could look like. We follow the principle [_release early, release often_](https://en.wikipedia.org/wiki/Release_early,_release_often) and aim at having a functional prototype of the search index at any time. We will use this resource to
* explore what kind of meta-data we need to collect for training materials
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[https://git.mpi-cbg.de/rhaase/lecture_working_with_objects_in_2d_and_3d](https://git.mpi-cbg.de/rhaase/lecture_working_with_objects_in_2d_and_3d)

## Research Data Management Seminar - Slides
By Della Chiesa, Stefano



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Expand Up @@ -754,6 +754,7 @@ <h2>Sharing Your Poster on Figshare: A Community Guide to How-To and Why<a class
</section>
<section id="running-deep-learning-scripts-in-the-bia-pol-omero-server">
<h2>Running Deep-Learning Scripts in the BiA-PoL Omero Server<a class="headerlink" href="#running-deep-learning-scripts-in-the-bia-pol-omero-server" title="Permalink to this heading">#</a></h2>
<p>By Marcelo Zoccoler</p>
<p><a class="reference external" href="https://biapol.github.io/blog/marcelo_zoccoler/omero_scripts/readme.html">https://biapol.github.io/blog/marcelo_zoccoler/omero_scripts/readme.html</a></p>
</section>
<section id="browsing-the-open-microscopy-image-data-resource-with-python">
Expand All @@ -762,6 +763,7 @@ <h2>Browsing the Open Microscopy Image Data Resource with Python<a class="header
</section>
<section id="getting-started-with-mambaforge-and-python">
<h2>Getting started with Mambaforge and Python<a class="headerlink" href="#getting-started-with-mambaforge-and-python" title="Permalink to this heading">#</a></h2>
<p>By Mara Lampert</p>
<p>Tags: python</p>
<p><a class="reference external" href="https://biapol.github.io/blog/mara_lampert/getting_started_with_mambaforge_and_python/readme.html">https://biapol.github.io/blog/mara_lampert/getting_started_with_mambaforge_and_python/readme.html</a></p>
</section>
Expand All @@ -771,6 +773,7 @@ <h2>Promoting Data Management at the Nikon Imaging Center and Cell Biology Micro
</section>
<section id="data-handling-in-large-scale-electron-microscopy">
<h2>Data handling in large-scale electron microscopy<a class="headerlink" href="#data-handling-in-large-scale-electron-microscopy" title="Permalink to this heading">#</a></h2>
<p>By Job Fermie</p>
<p><a class="reference external" href="https://blog.delmic.com/data-handling-in-large-scale-electron-microscopy">https://blog.delmic.com/data-handling-in-large-scale-electron-microscopy</a></p>
</section>
<section id="tracking-in-napari">
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</section>
<section id="research-data-management-seminar-slides">
<h2>Research Data Management Seminar - Slides<a class="headerlink" href="#research-data-management-seminar-slides" title="Permalink to this heading">#</a></h2>
<p>By Della Chiesa, Stefano</p>
<p><a class="reference external" href="https://zenodo.org/record/6602101">https://zenodo.org/record/6602101</a></p>
</section>
<section id="a-biologists-guide-to-planning-and-performing-quantitative-bioimaging-experiments">
<h2>A biologist’s guide to planning and performing quantitative bioimaging experiments<a class="headerlink" href="#a-biologists-guide-to-planning-and-performing-quantitative-bioimaging-experiments" title="Permalink to this heading">#</a></h2>
<p>By Rebecca A. Senft ,Barbara Diaz-Rohrer ,Pina Colarusso,Lucy Swift,Nasim Jamali,Helena Jambor,Thomas Pengo,Craig Brideau,Paula Montero Llopis,Virginie Uhlmann,Jason Kirk,Kevin Andrew Gonzales,Peter Bankhead,Edward L. Evans III,Kevin W. Eliceiri,Beth A. Cimini</p>
<p><a class="reference external" href="https://doi.org/10.1371/journal.pbio.3002167">https://doi.org/10.1371/journal.pbio.3002167</a></p>
<p><a class="reference external" href="https://www.bioimagingguide.org/">https://www.bioimagingguide.org/</a></p>
</section>
<section id="annotated-high-throughput-microscopy-image-sets-for-validation">
<h2>Annotated high-throughput microscopy image sets for validation<a class="headerlink" href="#annotated-high-throughput-microscopy-image-sets-for-validation" title="Permalink to this heading">#</a></h2>
<p>By Vebjorn Ljosa, Katherine L Sokolnicki, Anne E Carpenter</p>
<p>Broad Bioimage Benchmark Collection (BBBC)</p>
<p><a class="reference external" href="https://www.nature.com/articles/nmeth.2083">https://www.nature.com/articles/nmeth.2083</a></p>
<p><a class="reference external" href="https://bbbc.broadinstitute.org/">https://bbbc.broadinstitute.org/</a></p>
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Expand Up @@ -708,6 +708,7 @@ <h2> Contents </h2>
<h1>document<a class="headerlink" href="#document" title="Permalink to this heading">#</a></h1>
<section id="biapy-bioimage-analysis-pipelines-in-python">
<h2>BiaPy: Bioimage analysis pipelines in Python<a class="headerlink" href="#biapy-bioimage-analysis-pipelines-in-python" title="Permalink to this heading">#</a></h2>
<p>By Daniel Franco-Barranco et al</p>
<p>BiaPy is an open source Python library for building bioimage analysis pipelines, also called workflows.</p>
<p>Tags: python</p>
<p><a class="reference external" href="https://biapy.readthedocs.io/">https://biapy.readthedocs.io/</a></p>
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