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GloBIAS Launched!

Global Bioimage Analysts' Society (GloBIAS) officially launched on October 24th, 2024, aiming to promote a sustainable worldwide community of bioimage analysts. We registered the society in Austria. We compared the simplicity of the registration of a society in various countries, and the final choice was Austria. It was also that Gabriel Krens, the head of the imaging facility at the Institute of Science and Technology Austria (ISTA), kindly agreed to host the location of GloBIAS in his institute. We thank Gabriel tremendously for this generous support.

GloBIAS aims to support bioimage analysis experts, including analysts, software developers, and users of bioimage analysis. When we say “bioimage analysis”, it means “quantitative measurement of the parameters of biological systems using image data”. Nowadays, image data is more complex than what we generally perceive as “images” in our daily life. It is a form of data that captures the multidimensional state of biological systems. This means that the analysis of such data is beyond “image analysis” in the traditional sense - it is more about how we untangle that multidimensionality and come to some simpler view, looking at and understanding how biological systems are in operation. The future of this community is filled with many findings we have yet to know, and with excitement to explore the jungle of biological systems.

Bioimage Data Analysis Workflows ‒ Advanced Components and Methods

https://link.springer.com/book/10.1007/978-3-030-76394-7#toc

Since 2022, the third book from the NEUBIAS network has been available, with open access to all chapters. Enjoy!

Contents:

  • Introduction (Nataša Sladoje and Kota Miura)
  • Batch Processing Methods in ImageJ (Anna Klemm and Kota Miura)
  • Python: Data Handling, Analysis and Plotting (Arianne Bercowsky Rama)
  • Building a Bioimage Analysis Workflow Using Deep Learning (Estibaliz Gómez-de-Mariscal, Daniel Franco- Barranco, Arrate Muñoz-Barrutia and Ignacio Arganda-Carreras)
  • GPU-Accelerating ImageJ Macro Image Processing Workflows Using CLIJ (Daniela Vorkel and Robert Haase)
  • How to Do the Deconstruction of Bioimage Analysis Workflows: A Case Study with SurfCut. (Marion Louveaux and Stéphane Verger)
  • i.2.i. with the (Fruit) Fly: Quantifying Position Effect Variegation in Drosophila Melanogaster (Bertrand Cinquin, Joyce Y. Kao and Mark L. Siegal)
  • A MATLAB Pipeline for Spatiotemporal Quantification of Monolayer Cell Migration (Yishaia Zabary and Assaf Zaritsky)

Reproducible image handling and analysis

We often hear retraction of papers with fake image data like gel images with hand-drawn bands and cleanups, but in addition to such elementary-level mistakes, there are image analyses used in papers that are scientifically questionable. With Simon, we tried to shed light on this overlooked problem and propose a solution.

NEUBIAS Training School Paper

Details of motivations, the design, and paedagogic concepts of NEUBIAS Bioimage Analysis schools, started in 2017, are now in a manuscript. I wrote the “Bioimage Analyst School” part, and am quite satisfied to have the written record of our struggle and achievements, that I did together with the bioimage analysis genius Jean-Yves Tinevez (The Pasteur Institute, Paris).

F1000R NEUBIAS Gateway: Highlights from the 2016-2020 NEUBIAS training schools for Bioimage Analysts: a success story and key asset for analysts and life scientists

Bleach Correction Plugin Paper

The paper describing the Bleach Correction Plugin (for ImageJ) is now published.

https://f1000research.com/articles/9-1494

Please cite this paper if you are using this plugin!

Bioimage Data Analysis Workflow (2019) Springer

https://link.springer.com/book/10.1007/978-3-030-22386-1 We now have a new book "Bioimage Data Analysis Workflow"published from Springer, topics of which are centered around bioimage analysis workflows. The book is open access - thanks to the support from COST Action.

NeuBIAS Started!

As of May 3rd 2016, supported by COST grant, NeuBIAS officially launched for creating a stronger and broader network among bioimage analysts: read "EuBIAS Manifesto (2013, DOI:10.5281/zenodo.18047)" for more details about our initial motivation. The official document stating our activities is here (PDF)

BIAS has been a small group, and EuBIAS has been a bit larger but now with NeuBIAS, it's big!

BIAS 2016

EMBL Master Course for Bioimage Data Analysis (BIAS2016): Registration is now open, deadline on April 15th.

Official Website: http://www.embl.de/bias2016

Course Wiki: BIAS2016 wiki

Published: Bioimage Data Analysis

A new book is now online: “Bioimage Data Analysis”. The instructors of EMBL Bioimage Data Analysis coauthored 10 chapters on practical techniques for analyzing image data in biology. E-books are downloadable free of charge from the following link.

Bioimage Data Analysis (2016), Wiley-VCH

For sample image data and codes, please download from the following link:

Bioimage Data Analysis: Materials

Triweekly CMCI image analysis seminar launched

The CMCI seminar has been either spontaneous or took a form of mini-symposium, but now in a new format.

Every three weeks, seminar member gathers and two of them present image analysis problems / solutions or reads a paper. For more details and the schedule, see this page.

start.txt · Last modified: 2025/05/16 09:35 by kota

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