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Imaggeo on Mondays: A slice of fossil life

Imaggeo on Mondays: A slice of fossil life

I am a petrographer at the University of Padova, Italy, studying the metamorphic rocks that form the deep Earth’s crust beneath our feet, and what happens when they get so hot to start to melt.

I’ve spent (enjoyed I should say) more than 30 years looking at rocks with an optical microscope. This simple, cheap tool, and more importantly, its skilled use, remain key ingredients for good research in petrology!

I’ve been taught by scientists, like Ron Vernon of Macquarie University in Australia, that a good micrograph is essential to document my research and strengthen my conclusions, and so I’ve always paid particular attention to the quality of photos. In the meanwhile, I have also developed a particular interest in photomicroscopy with an aesthetic purpose, realizing that the cocktail of rocks and polarized light has an extraordinary potential in the ‘sciart’ (Science-and-Art) field.

The digital revolution has marked a turning point in this activity, and 10 years ago I have started my micROCKScopica project to showcase to the public the beauty hidden in the small slices of rock that are thin sections.

When I find a photogenic rock I play with polarizers to get the desired combinations of color, and then I take a photograph. And people can enjoy the images, their colors and shapes, even without knowing the geological history behind them.

This is particularly true for this photograph: it is a thin section of a piece of dinosaur bone but I don’t know much about it (what bone, which dinosaur), only that it had been collected in Utah, in the United States. I received a small sample of the bone by Denise M. Harrison, a friend with whom I collaborated for a book on Lake Superior Agates. She is an award-winning lapidary (someone who cuts, polishes and engraves stones), and makes lovely cabochons with all sort of semiprecious, hard stones. I asked her for some leftovers to make some thin sections, because I wanted to see something new, possibly silicified (impregnated with silica during fossilization) because chalcedony – the very fine-grained variety of common quartz – may be extremely photogenic.

I had no idea of how a bone could look like under the microscope, and the first sight left me speechless! The porous structure, and the patterns of the radiating textures in the chalcedony fillings are extraordinary, and provide a wealth of possibilities for nice images.

In this shot, that I replicated in red and blue, a larger hole had been filled with a fine-grained quartz sand – the dark moon shape on top left – somehow interrupting the regular pattern of the bone tissue, that to someone may recall Australian Aboriginal artwork.

Curiously, this anatomically-related image made me quite popular among pathologists and other medical doctors, who find many analogies with their subjects of research. The ages of the specimens are some hundred million years apart, though…

By Bernardo Cesare, University of Padova, Italy

Editor’s note: The fossil sample featured in this photo was collected and distributed legally from Utah.

If you pre-register for the 2019 General Assembly (Vienna, 07–12 April), you can take part in our annual photo competition! From 15 January until 15 February, every participant pre-registered for the General Assembly can submit up three original photos and one moving image related to the Earth, planetary, and space sciences in competition for free registration to next year’s General Assembly!  These can include fantastic field photos, a stunning shot of your favourite thin section, what you’ve captured out on holiday or under the electron microscope – if it’s geoscientific, it fits the bill. Find out more about how to take part at

Imaggeo is the EGU’s online open access geosciences image repository. All geoscientists (and others) can submit their photographs and videos to this repository and, since it is open access, these images can be used for free by scientists for their presentations or publications, by educators and the general public, and some images can even be used freely for commercial purposes. Photographers also retain full rights of use, as Imaggeo images are licensed and distributed by the EGU under a Creative Commons licence. Submit your photos at

Iceland’s rootless volcanoes

Iceland’s rootless volcanoes

Picture a volcano, like the one you learned about in primary school. Can you see it? Is it a big rocky mountain, perhaps with a bubbling pool of lava at the top? Is it perched above a chasm of subterranean molten rock?

I bet you didn’t picture this:

Rootless cones in the Lanbrotshólar district, S Iceland. Created by the 940AD Eldgjá eruption, there are over 4000 rootless cones in this area. Credit: Frances Boreham

You’d be forgiven for mistaking these small volcanoes for a scene from the Lord of the Rings, or maybe a grassy version of the surface of Mars (in fact, these kind of volcanoes do occur on Mars). These, however, are in Iceland and are called rootless cones.

These mini-volcanoes are unusual because they are ‘rootless’ meaning, unlike most volcanoes, they are not fed from the underground. To make them even stranger, they erupted only once and as part of the same event.

This type of volcanism is observed in several places around the world and occurs only in a unique set of circumstances. Despite showing similarities to more traditional volcanoes (like pyroclastic cones), the cones pictured above actually erupted several tens of kilometres from a ‘true’ volcano.

Rootless cones occur when a hot lava flow produced by an eruption travels away from the volcano and meets water. This can be a lake, a river, a glacier or simply a bit of soggy ground. The only criteria are that there needs to be water, and it needs to be trapped. Lava flows are usually at temperatures of over 1000oC and so, when they come into contact with trapped water or ice, its causes a build-up of steam, which can explode violently through the lava forming a rootless cone.

An article, published in the Journal of Volcanology and Geothermal Research in September by volcanologists from the University of Bristol and the University of Iceland, analysed the shape and location of some of these cones to understand more about the environment in which they formed.

These features are found in northeast Iceland in the region around lake Mývatn. The area, 50 km east of the city of Akureyri, is world famous for its beautiful scenery and unusual landscapes.

The volcano responsible for the phenomena is the Þrengslaborgir–Lúdentsborgir crater row which erupted around 2000 years ago. The eruption produced a huge lava flow that covered an area of 220 km2; over 2% of the surface of Iceland. The flow, known as the Younger Laxá Lava, permanently changed the landscape, diverting rivers and damming lakes. After its extrusion from the volcano, the stream of molten rock meandered through different environments including river gorges and wide glacial valleys.

The flow’s diverse 67km journey allowed lead author Frances Boreham and her colleagues, to learn how it interacted with its surroundings. As she explains it, “one of the things that makes the Younger Laxá Lava such a great case study is the range of environments that the lava flowed through.”

Rootless cones do not all look the same and vary greatly in size, from small ‘hornitos’ which are about the size of a small car, to large crater-shaped cones hundreds of metres in size. The scale and complexity of the deposits makes them difficult to study as Boreham explains, “One of the biggest challenges is trying to understand and unpick the different effects of lava and water supply on rootless eruptions. We see a huge variety in rootless cone shapes and sizes, but working out which aspects are controlled by the lava flow and which by the environment and available water is tricky, especially when working on a lava flow that’s approximately 2000 years old!”

From Boreham et al. 2016. “Different types of rootless cone and associated features. a) Scoriaceous rootless cone at Skutustaðir, Mývatn. Cone base is ~100 m diameter. b) Explosion pits (marked with arrows) surrounding a scoriaceous rootless cone near Mývatn. c) Spatter cone at Mý d) Hornito in Aðaldalur, NE Iceland. Map imagery on d ©2017 DigitalGlobe, Google.” Licensed under creative commons.

Despite their beauty, the rootless cones represent a more serious issue. Lava flows are often thought of as quite benign compared to other volcanic hazards like pyroclastic flows. The presence of rootless cones suggests this isn’t always the case. “As far as I know, none of these rootless cones are currently taken into account for lava flow hazard assessments, in Iceland or elsewhere in the world. While not applicable everywhere, wet environments with a history of lava flows, such as Iceland or parts of the Cascades, could be affected and these hazards should be considered in future risk assessments and plans, e.g. by identifying vulnerable property, roads and infrastructure.” said Boreham.

By Keri McNamara, freelance science writer

Keri McNamara is a freelance writer with a PhD in Volcanology from the University of Bristol. She is on twitter @KeriAMcNamara and

Imaggeo on Mondays: An iceberg-sized issue

Imaggeo on Mondays: An iceberg-sized issue

This was taken during a study, undertaken by me and my colleagues, on the sea ice of McMurdo Sound, Antarctica. We designed the project to document how supercooled water carrying suspended ice crystals flows along its pathway towards the open ocean. Ultimately, this work aims to assess the Ross Ice Shelf’s contribution of local melt to the long-term trend of increased sea ice cover around Antarctica – a signal which has been dominated by expansion in the Ross Sea.

However, over the winter prior to the field season an iceberg, 12 kilometres long and 1 kilometre wide that had calved from the Ross Ice Shelf, grounded itself across the middle of our intended study region. This created a significant constriction to the flow, as the iceberg forced the approximately 30 km-wide plume to squeeze into half of that space.

We quickly modified the objectives for the field season to take advantage of this, adding an element focusing on the fluid dynamics of accelerated large-scale flow around the tip of the iceberg, and another on the thermodynamics of the supercooled plume interacting with a deep wall of ice. These adjustments to our study required drilling several holes through the sea ice along lines that approached the iceberg from two different directions to collect the necessary oceanographic data.

The iceberg towers about 40 m above the frozen sea surface, with our field support team providing scale as they scope a route of safe approach. However, hidden from sight by the sea ice, the iceberg stretches a further 170 m below the surface to the point where it is grounded on the seafloor.

Conducting field science in Antarctica requires being able to adapt to a dynamic environment. In this case, our flexibility was rewarded with a unique data set – essentially a laboratory study in fluid mechanics on a real-world scale.

By Natalie Robinson, New Zealand National Institute for Water and Atmospheric Research (NIWA)

If you pre-register for the 2019 General Assembly (Vienna, 07–12 April), you can take part in our annual photo competition! From 15 January until 15 February, every participant pre-registered for the General Assembly can submit up three original photos and one moving image related to the Earth, planetary, and space sciences in competition for free registration to next year’s General Assembly!  These can include fantastic field photos, a stunning shot of your favourite thin section, what you’ve captured out on holiday or under the electron microscope – if it’s geoscientific, it fits the bill. Find out more about how to take part at

Imaggeo is the EGU’s online open access geosciences image repository. All geoscientists (and others) can submit their photographs and videos to this repository and, since it is open access, these images can be used for free by scientists for their presentations or publications, by educators and the general public, and some images can even be used freely for commercial purposes. Photographers also retain full rights of use, as Imaggeo images are licensed and distributed by the EGU under a Creative Commons licence. Submit your photos at

How to increase reproducibility and transparency in your research

How to increase reproducibility and transparency in your research

Contemporary science faces many challenges in publishing results that are reproducible. This is due to increased usage of data and digital technologies as well as heightened demands for scholarly communication. These challenges have led to widespread calls for more research transparency, accessibility, and reproducibility from the science community. This article presents current findings and solutions to these problems, including recent new software that makes writing submission-ready manuscripts for journals of Copernicus Publications a lot easier.

While it can be debated if science really faces a reproducibility crisis, the challenges of computer-based research have sparked numerous articles on new good research practices and their evaluation. The challenges have also driven researchers to develop infrastructure and tools to help scientists effectively write articles, publish data, share code for computations, and communicate their findings in a reproducible way, for example Jupyter, ReproZip and research compendia.

Recent studies showed that the geosciences and geographic information science are not beyond issues with reproducibility, just like other domains. Therefore, more and more journals have adopted policies on sharing data and code. However, it is equally important that scientists foster an open research culture and teach researchers how they adopt more transparent and reproducible workflows, for example at skill-building workshops at conferences offered by fellow researchers, such as the EGU short courses, community-led non-profit organisations such as the Carpentries, open courses for students, small discussion groups at research labs, or individual efforts of self-learning. In the light of prevailing issues of a common definition of reproducibility, Philip Stark, a statistics professor and associate dean of mathematical and physical sciences at the University of California, Berkeley, recently coined the term preproducibility: “An experiment or analysis is preproducible if it has been described in adequate detail for others to undertake it.” The neologism intends to reduce confusion and also to embrace a positive attitude for more openness, honesty, and helpfulness in scholarly communication processes.

In the spirit of these activities, this article describes a modern workflow made possible by recent software releases. The new features allow the EGU community to write preproducible manuscripts for submission to the large variety of academic journals published by Copernicus Publications. The new workflow might require hard-earned adjustments for some researchers, but it pays off because of an increase in transparency and effectivity. This is especially the case for early career scientists. An open and reproducible workflow enables researchers to build on others’ and own previous work and better collaborate on solving the societal challenges of today.

Reproducible research manuscripts

Open digital notebooks, which interweave data and code and can be exported to different output formats such as PDF, are powerful means to improve transparency and preproducibility of research. Jupyter Notebook, Stencila and R Markdown let researchers combine long-form text of a publication and source code for analysis and visualisation in a single document. Having text and code side-by-side makes them easier to grasp and ensures consistency, because each rendering of the document executes the whole workflow using the original data. Caching for long-lasting computations is possible, and researchers working with supercomputing infrastructures or huge datasets may limit the executed code to purposes of visualisation using processed data as input. Authors can transparently expose specific code snippets to readers but also publish the complete source code of the document openly for collaboration and review.

The popular notebook formats are plain text-based, like Markdown in case of R Markdown. Therefore an R Markdown document can be managed with version control software, which are programs for managing multiple versions and contributions, even by different people, to the same documents. Version control provides traceability of authorship, a time machine for going back to any previous “working” version, and online collaboration such as on GitLab. This kind of workflow also stops the madness of using file names for versions yet still lets authors use awesome file names and apply domain-specific guidelines for packaging research.

R Markdown supports different programming languages besides the popular namesake R and is a sensible solution even if you do not analyse data with scripts nor have any code in your scholarly manuscript. It is easy to write, allows you to manage your bibliography effectively, can be used for websites, books or blogs, but most importantly it does not fall short when it is time to submit a manuscript article to a journal.

The rticles extension package for R provides a number of templates for popular journals and publishers. Since version 0.6 (published Oct 9 2018) these templates include the Copernicus Publications Manuscript preparations guidelines for authors. The Copernicus Publications staff was kind enough to give a test document a quick review and all seems in order, though of course any problems and questions shall be directed to the software’s vibrant community and not the publishers.

The following code snippet and screen shot demonstrate the workflow. Lines starting with # are code comments and explain the steps. Code examples provided here are ready to use and only lack the installation commands for required packages.

# load required R extension packages:

# create a new document using a template:
rmarkdown::draft(file = "MyArticle.Rmd",
                 template = "copernicus_article",
                 package = "rticles", edit = FALSE)

# render the source of the document to the default output format:
rmarkdown::render(input = "MyArticle/MyArticle.Rmd")

{: .language-r}

The commands created a directory with the Copernicus Publications template’s files, including an R Markdown (.Rmd) file ready to be edited by you (left-hand side of the screenshot), a LaTeX (.tex) file for submission to the publisher, and a .pdf file for inspecting the final results and sharing with your colleagues (right-hand side of the screenshot). You can see how simple it is to format text, insert citations, chemical formulas or equations, and add figures, and how they are rendered into a high-quality output file.

All of these steps may also be completed with user-friendly forms when using RStudio, a popular development and authoring environment available for all operating systems. The left-hand side of the following screenshot shows the form for creating a new document based on a template, and the right-hand shows side the menu for rendering, called “knitting” with R Markdown because code and text are combined into one document like threads in a garment.

And in case you decide last minute to submit to a different journal, rticles supports many publishers so you only have to adjust the template while the whole content stays the same.

Sustainable access to supplemental data

Data published today should be published and properly cited using appropriate research data repositories following the FAIR data principles. Journals require authors to follow these principles, see for example the Copernicus Publications data policy or a recent announcement by Nature. Other publishers required, or still do today, to store supplemental information (SI), such as dataset files, extra figures, or extensive descriptions of experimental procedures, as part of the article. Usually only the article itself receives a digital object identifier (DOI) for long-term identification and availability. The DOI minted by the publisher is not suitable for direct access to supplemental files, because it points to a landing page about the identified object. This landing page is designed to be read by humans but not by computers.

The R package suppdata closes this gap. It supports downloading supplemental information using the article’s DOI. This way suppdata enables long-term reproducible data access when data was published as SI in the past or in exceptional cases today, for example if you write about a reproduction of a published article. In the latest version available from GitHub (suppdata is on its way to CRAN) the supported publishers include Copernicus Publications. The following example code downloads a data file for the article “Divergence of seafloor elevation and sea level rise in coral reef ecosystems” by Yates et al. published in Biogeosciences in 2017. The code then creates a mostly meaningless plot shown below.

# load required R extension package:

# download a specific supplemental information (SI) file
# for an article using the article's DOI:
csv_file <- suppdata::suppdata(
  x = "10.5194/bg-14-1739-2017",
  si = "Table S1 v2 UFK FOR_PUBLICATION.csv")

# read the data and plot it (toy example!):
my_data <- read.csv(file = csv_file, skip = 3)
plot(x = my_data$NAVD88_G03, y = my_data$RASTERVALU,
     xlab = "Historical elevation (NAVD88 GEOID03))",
     ylab = "LiDAR elevation (NAVD88 GEOID03)",
     main = "A data plot for article 10.5194/bg-14-1739-2017",
     pch = 20, cex = 0.5)

{: .language-r}

Main takeaways

Authoring submission-ready manuscripts for journals of Copernicus Publications just got a lot easier. Everybody who can write manuscripts with a word processor can learn quickly R Markdown and benefit from a preproducible data science workflow. Digital notebooks not only improve day-to-day research habits, but the same workflow is suitable for authoring high-quality scholarly manuscripts and graphics. The interaction with the publisher is smooth thanks to the LaTeX submission format, but you never have to write any LaTeX. The workflow is based on an established Free and Open Source software stack and embraces the idea of preproducibility and the principles of Open Science. The software is maintained by an active, growing, and welcoming community of researchers and developers with a strong connection to the geospatial sciences. Because of the complete and consistent notebook, you, a colleague, or a student can easily pick up the work at a later time. The road to effective and transparent research begins with a first step – take it!


The software updates were contributed by Daniel Nüst from the project Opening Reproducible Research (o2r) at the Institute for Geoinformatics, University of Münster, Germany, but would not be able without the support of Copernicus Publications, the software maintainers most notably Yihui Xie and Will Pearse, and the general awesomeness of the R, R-spatial, Open Science, and Reproducible Research communities. The blog text was greatly improved with feedback by EGU’s Olivia Trani and Copernicus Publications’ Xenia van Edig. Thank you!

By Daniel Nüst, researcher at the Institute for Geoinformatics, University of Münster, Germany

[This article is cross posted-on the Opening Reproducible Research project blog]