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The NEUBIAS Gateway has had a great first year, with 26 articles published since we launched the Gateway on 16^th June 2020. The Gateway was created with the primary aim of being a knowledge hub for bioimage analysts, enabling researchers to share their efforts in a field that has been lacking a central place to publish.

Today, we will be looking at the most read articles to come out of the Gateway and the impact they’ve had on their communities.

The frontrunner

Effective image visualization for publications – a workflow using open access tools and concepts

Having already featured in our blog as the top Tweeted article in 2020, this workflow by Helena Jambor and Christopher Schmied has received the most views and downloads as well as the highest Altmetric score in the Gateway. This is partly thanks to a well-received Tweet by Christopher Schmied, showing the value of authors promoting their work on social media. The authors told us more about their work in a blog post earlier this year where they also highlighted the importance of open peer review in providing opportunities for discussion.

This Software Tool article takes you through a workflow to process and prepare images for publication and is made specifically with novices in mind, using easy-to-follow cheat sheets. However, as reviewer Guillaume Jacquemet (University of Turku, Finland) says, this article “will be very useful for students and seasoned microscopists alike”. From the discussions on Twitter, it seems this will be recommended reading for some time to come! In fact, the authors welcome translations of the cheat sheets to further expand its reach.

Most read Software Tool Articles

Automated cell tracking using StarDist and TrackMate

“Overall, this is a clear description of several powerful tools being combined into a very useful and versatile workflow”

Lachlan W. Whitehead, The Walter and Eliza Hall Institute of Medical Research, Australia

Cell migration has been studied for over 50 years, yet despite software being available, most researchers still use manual methods. The authors suggest this is because of the difficulty in setting up robust automated cell tracking and large-scale analysis.

In this Software Tool Article, they provide an automated pipeline for cell tracking using a combination of open source tools. With over 1,200 views and 200 downloads, this Software Tool Article has been well-read and well-received.

Interactive biomedical segmentation tool powered by deep learning and ImJoy

“As it is, the tool should be seen as an important stepping stone towards a truly interactive training paradigm for experimentalists”

Jan Funke, Howard Hughes Medical Institute, USA

In this Software Tool Article the authors present a new ImJoy plugin which allows users to train a deep learning model by manually annotating images.

The authors demonstrate how to use the tool with a recording embedded as a widget within the article, so readers can hit play and watch the video within the article itself.  It’s great to see authors using the functionality we offer within the article pages of our platform.

Want to see more research like this? Click here to read all the software tool articles published in the NEUBIAS Gateway.

Top Opinion Article

Developing open-source software for bioimage analysis: opportunities and challenges

There can often be a disconnect between computer scientists and life scientists when it comes to bioimage analysis. This gap is typically filled by a specialist bioimage analyst, someone who identifies and adapts software tools for the biological question at hand. However, not all facilities employ a specialist and not all life scientists have the resources to develop workflows for bioimage analysis.

In this paper, the authors discuss the challenges of developing open source software for bioimage analysis, from its inception to maintenance, documentation, and more. They hope this will be beneficial both to developers and users so that the gap might be closed, and all parties will have a better understanding of what is needed to create and support successful software.

Looking for more Opinion Articles? Click here to read all the Opinion Articles published in the NEUBIAS Gateway.

Looking forward

The NEUBIAS Gateway will continue to publish work that contributes to the development of bioimage analysis including image processing, analysis, visualization and statistical methods, bioimage analysis workflows, software packages, machine learning based approaches, data mining architecture and storage management, and more.

We strongly encourage submissions from the community at any time. If you have any questions or feedback, feel free to get in touch.