New image analysis training school with Neubias

NEUBIAS, the Network of European BioImage Analysts, is delighted to announce two new Training Schools on BioImage Analysis:

TS14 for Early Career Investigators (Life Scientists: PhD candidates, Postdocs, Staff, …):

This training school will cover the basics of image analysis using ImageJ/Fiji, as well as image analysis workflow automation using ImageJ macro programming. In addition, it will be taught how to use the software package ilastik for machine learning based image segmentation and object classification, and how to integrate ilastik into ImageJ macro based workflows. Moreover, an overview of further relevant bioimage analysis software packages will be given and there will be ample time for “Work on Your Own Data” sessions assisted by experienced Analysts.

TS15 for BioImage Analysts (advanced level):

This school targets bioimage analysts, who are willing to enhance their professional scope and techniques for improving the quality of their analysis, at the same time as willing to contribute with their knowledge and experience to the school. Prerequisite is a proficiency in at least one programming language (we do not train coding). The school focuses on workflow designing. This year, we will have a particular emphasis on statistics for bioimage analysis and related tools e.g. R and Python libraries. In addition, we will overview machine & deep learning components.

The schools will be held in Bordeaux, Feb 29 – Mar 03 2019, hosted at the Centre Broca Nouvelle-Aquitaine by the Bordeaux Imaging Center (BIC) and the Interdisciplinary Institute for Neuroscience. The selected students will be able to attend the whole NEUBIAS conference as part of the training.

NEUBIAS schools are an excellent opportunity to learn from many experts in Bioimage Analysis (we are expecting >20 specialists at the event) and “…a great mix of intensive learning and community networking” (former trainee testimonial). All schools include practical sessions “Work on Your Own Data”, plenary seminars and a session on ethics in image analysis.

Applications are now open (TS14 = 25 seats, TS15 = 35 seats and ~10+ trainers per school). Within the COST framework (funders of NEUBIAS), we will offer up to 7 travel grants per school to applicants who qualify.

Application deadline: December 12th 2019 Selection notification: December 20th 2019

More information about schools (programme & trainers) and venue, travel & lodge available at our website:

eubias.org/NEUBIAS/training-schools/

eubias.org/NEUBIAS/training-schools/eci/ts14-bordeaux-2020/

eubias.org/NEUBIAS/training-schools/analysts/ts15-bordeaux-2020/

We kindly ask that you help us reach out to all potential interested applicants.

on behalf of all NEUBIAS members, local organizers (Florian Levet and Fabrice Cordelières), scientific organizers (Romain Guiet, Elnaz Fazeli, Christian Tischer, Kota Miura, Marion Louveaux), and NEUBIAS Training Leaders Gabriel Martins and Fabrice Cordelières.

How to precisely measure the volume of a cell?

Measuring the volume of a cell is often done by labelling the cell membrane or its cytoplasm. Analysing large flat cells this way is easy but it is much harder for tiny cells like blood cells, yeast or bacteria.

Another way to measure volumes is to use a negative stain, i.e. where the medium is made fluorescent with a dye that does not go into the cell. The cell appears as a black hole in fluorescent images and unlike lipid-based membrane labelling, borders are even and easy to segment.

While many dyes can be used for live cells, one must choose large dyes when negatively imaging cells that have been fixed and permeabilized.

This paper and this one use high molecular weight (2000 KDa) Dextran to achieve these results and measure the size of bacteria.

This recent paper optimizes the technique.

 

Free genetic and image analysis tools

Here are a few image analysis tools (constructs for FRET, software…) that might be useful to you.

  • Construct for fluorescence biosensors and optogenetic tools
  • Free Image analysis software

http://www.hahnlab.com/tools/index.html

  • Free Image analysis software

https://www.utsouthwestern.edu/labs/danuser/software/

  • Free Image analysis software

http://cismm.web.unc.edu/

How to identify cells and nuclei in an image?

NucleAlzer is a great new deep learning tool to identify roundish objects like nuclei and cells in fluorescent or bright field images.

To test if the tool works for you before you download it, you can simply upload one of your images and check the result. Easy! 😀

Call4Help: fast-track help with your image analysis project!

BII (BioImage Informatics, the great image analysis at SciLife Uppsala) and the LCI facility will run a new Call4Help on the 4th of September.

Anyone who is stuck with image analysis and wishes for quick help to build a pipeline should apply. You don’t have to acquire the images at the LCI. Anyone can apply.

How does it work? You first upload your images and a little explanation text. A few days later, we all meet virtually in a Zoom chatroom for a quick (30 min-1 h) online session. You get comments, suggestions and help with building a Fiji or CellProfiler analysis pipeline tailor-made for your images.

If you are interested, click on the link below to apply:

BioImage Informatics

Imaging Africa workshop

Great initiative from the other side of the pond. Please forward to your imaging friends/colleagues working in African universities:

—————————————————–

We are pleased to announce Imaging Africa—a workshop initiative aimed at developing the microscopy knowledge and expertise of African life scientists.

Imaging Africa is an intensive, 4-day workshop + 1-day symposium focused on exposing students to a plethora of microscope technologies and impactful applications. Topics range from portable, cellphone-based microscopes to advanced super-resolution modalities. Furthermore, students will be introduced to experimental applications such as biosensors and optogenetic tools. These theoretical and practical classes will run in parallel with an in-depth quantitative image analysis course, which will provide the students with the skills necessary to reveal meaningful information from microscopy data.

With the generous support from the Gordon and Betty Moore Foundation, the Chan Zuckerberg Initiative, the Howard Hughes Medical Institute Janelia Research Campus and UNC-Chapel Hill, the Imaging Africa workshop is free of financial burden to all attending students. The expenses associated with air travel, accommodation, and food will be covered by Imaging Africa. Eligible applicants must currently be at an academic institution in the continent of Africa.

The workshop will be hosted at the University of Cape Town’s Institute of Infectious Disease and Molecular Medicine, South Africa from the 13th to the 16th of January 2020 and will be followed by a research symposium on the 17th of January 2020. Please visit www.imagingafrica.org for more information. Applications for the workshop close on the 15th of October 2019.

Please help us in making a meaningful impact on African researchers by forwarding this information to your friends and colleagues from any and all African institutions.

Sincerely,

Teng-Leong Chew, HHMI Janelia Research Campus, USA Dan Fletcher, Univ of California-Berkeley, USA Klaus Hahn, Univ of N. Carolina-Chapel Hill, USA Musa Mhlanga, Univ of Cape Town, S. Africa Kelly Rogers, Walter & Eliza Hall Institute, Australia Digby Warner, Univ of Cape Town, S. Africa

Neubias school for image analysis 2020

Neubias is a European effort to get biologists to analyse their images by locking them in a room with some image analysis experts. If you get accepted to the Neubias school, you get to learn image analysis on your own data and you get expert help to build your pipeline!

The next Neubias school will be in the beautiful city of Bordeaux in February 2020. Apply soon not to be disappointed! 🙂

Great help with image analysis: application deadline tomorrow!

Tomorrow 30th of May is the last day to apply to the Neubias (Network of Bioimage Analysts) image analysis school in Porto in October!

If you have any scary image analysis problem sitting under your bed at night, Neubias is for you 😉

Neubias is a great opportunity to get started/go deeper with image analysis and get your analysis pipeline written by experts.

Imaris workshop at the LCI: rescheduled to the 22nd of May :)

Imaris is a great image analysis software that is available to all the members of the Live Cell Imaging facility.

It is as easy to analyse 2D and 3D image files with Imaris. The software also allows you to make great multidimensional plots to present your data.

One can count objects inside objects (example number of vesicles per cell), measure shortest distances from one type of object to another (example distance from vesicles to the cell membrane), track cells even when they divide, trace neurons or blood vessels… all this in 3D, time, several colours.

On the 22nd of May, the LCI will host an Imaris workshop.

The morning seminar (held in Neo/DNA room) from 10-12 will be broadcasted for those who cannot join. Please follow the instructions on our website to follow the webinar.

In the afternoon, we will analyse the data of our users. Submit your images to DONTCHEVA Guergana (g.dontcheva(at)bitplane.com).

Call4Help: The image analysis help you have always dreamt of, totally for free!!! ???

After the success of the previous Call4Help session in February, BII (BioImage Informatics, the great image analysis at SciLife Uppsala) and your favorite microscopy facility (we hope) will run a new Call4Help next Tuesday 2nd of April.

Anyone who is stuck with image analysis and wishes for quick help can apply.

These are 100% online sessions (we ‘meet’ in a Zoom chat room) where you submit your images and a little explanation text in advance and you get suggestions for 30 min and an analysis pipeline all done for you (Fiji, CellProfiler, Ilastik, QuPath, KNIME)!

If you are interested, please apply as soon as possible (sorry for the late announcement).

Here is how to apply: https://www.scilifelab.se/facilities/bioimage-informatics/