ImageJ course London 8-9 May

Dear list, I've been running a 2 day ImageJ course for a few years now and would like to open this up for wider attendance. Course details and link to booking: Anonymous user feedback (over 200 attendees, 99 responses) gives a 100% recommended score, and you can read anonymous user comments here: Fees are : £50 UCL, £75 other academic, £100 non-academic. Free for ICH imaging facility users. I run the course every 3 months. Cheers Dale

ImageJ/Fiji workshops 15-16 July Leicester UK (Kees Straatman)

Dear All, I would like to announce the next ImageJ workshops I organize in Leicester, UK. Monday 15 July: Introduction to ImageJ/Fiji.Tuesday 16 July: Writing macros in ImageJ. The workshops are a mixture of lectures and hands-on sessions. No prior knowledge of ImageJ, Fiji or macro coding is required, only basic use of a laptop. For further information and registration please visit: Best wishes Kees——————————————————————————————— 

[RSE] Registration Open  | RSE Conference 2018 – 3rd & 4th September – University of Birmingham

We are pleased to announce that registration for the RSE Conference 2018 is now open at the following link:
The last two conferences sold out, so we’ve added 50% more tickets this year. However, there are already 300 people on the notification list, so it looks like we will sell out again this year. If you want to attend, we recommend that you sign up early. 
We have a great programme of talks, workshops and keynotes planned around the following themes:
* Good practice for software development
* Researcher-developer partnerships
* Community and careers
* Novel technologies and methods
* Software engineering toys, tips and tricks
The conference will kick off on Monday 3rd September with registration from 08:30 to 09:30 and the last session will wrap up at 17:30. A conference dinner sponsored by Microsoft will be held that evening in the Great Hall at 19:30 starting with a drinks reception at 19:00.  The conference will continue on Tuesday 4th September with registration for anyone who hasn’t registered on Monday at 08:30, with sessions starting at 09:30 and will close at 17:30.  Information on some of the workshops is already available:  We’re working hard on the full programme which will be published soon.
We have confirmed keynotes from:
* Eleanor Robson, Professor of Ancient Middle Eastern History –
* James Howison, Associate Professor in the Information School of the University of Texas at Austin –
* Andrew Fitzgibbon, Partner Scientist, HoloLens, Microsoft –
Great Hall Exhibitors
Without our sponsors, the RSE conference couldn’t exist. Our sponsors are also our exhibitors and this year we’ve expanded our exhibitor hall and will be welcoming Microsoft, Google, Intel, Wellcome Trust, Amazon Web Services, Mathworks, STFC, SSI, Eclipse Foundation, CANARIE, NAG and EPSRC.

The University of Birmingham are holding rooms available for booking in the Chamberlain Halls that are a 25 minute walk from the conference venue. Rooms are £54 per room per night.  Booking is possible via a link on theRSE Conference website. Click on the green ‘Book Accommodation’ link and you will be redirected to the University of Birmingham website. Accommodation is available to book for the Sunday 2nd, Monday 3rd and Tuesday 4th September. It is the responsibility of the attendee to book accommodation, separately from the conference registration.

Citation File Format Hackday – Wednesday 5th September 2018

Stay on an extra day to participate in this hackday.  During this dedicated Hack Day, we want to: Give an overview of – and discuss – the Citation File Format, its tooling and workflows; Discuss what tools would be necessary to facilitate, e.g., better usability, optimized workflows, or integration with other tools in the software citation workflow (reference managers, repositories, other formats, etc.); Do some actual work around existing and new tools, as well as the Citation File Format itself and its documentation. Find out more

Presenters Registration
For Talk, Workshop and Poster presenters, you will be sent a separate link soon to register for the conference.Please note that one lead presenter per talk, workshop or poster will be able to register via the presenter link.All other presenters in your team must register using the delegate registration, linked above.
If you have applied to participate in the conference as a volunteer, you will be notified by Friday 8th June whether your application has been successful or not and will then receive a dedicated volunteer registration link next week.
To contact the conference committee, please email and the relevant Chair will respond. We look forward to welcoming you to the RSE Conference 2018.
RSE 18 Organising Committee

Call for papers: Bioimage Computing @ ECCV 2018

Call for papers: Bioimage Computing @ ECCV 2018

Bio-image computing (BIC) emerges as a rapidly growing field on the interface between engineering, biology and computer science. State-of-the-art light microscopy (LM) can deliver 2D and 3D image sequences of living cells with unprecedented image quality and ever growing resolution in space and time. The emergence of novel and quite diverse LM modalities has provided biologists with formidable means to explore cell mechanisms, embryogenesis, or neural development, to quote just a few fundamental biological issues. Electron microscopy (EM) supplies information on the cell structure down to the nanometer resolution. Correlating LM and EM at the microscopic level, and both with animal behavior at the macroscopic level, is of paramount importance. In the face of huge data sets, at a size of multiple TB per volume or video, and exceedingly difficult problems, state-of-the-art computer vision are required and need to be further developed.

Paper Submission: 2. Jul. 2018
Decision Notifications: 6. Aug. 2018
Camera Ready Deadline: After the workshop
Workshop: 14. Sep. 2018

Relevance to the computer vision community. This workshop will bring the latest challenges in bio-image computing to the computer vision community. At the same time it will showcase the specificities of bio-image computing and its current achievements, including issues related to image modeling, denoising, super-resolution, multi-scale segmentation, motion estimation, image registration, tracking, classification, event detection — important topics that appertain to the computer vision field.

Topics of interest include:

LM and EM image restoration and reconstruction
Reproducible image analyses over terabyte-sized images
Deep learning for bioimaging
3D registration
Segmentation of subcellular objects, cells, and animals (instances and classes)
Multimodal image analysis (correlative LM and EM, various LM modalities)
Analysis of motion: particle tracking and tracking of cells, tissues, and organisms
Automated behavior recognition
Dense motion estimation in 2D and 3D LM image sequences
Diffusion computation
Statistical analysis of (object) shape
Image-based phenotyping
Evaluation and benchmarking methodologies of automated image algorithms/pipelines
Interactive image analyses (of gigapixel images)
Creating large collections of labeled training datasets
other technically interesting and biologically useful pipelines and algorithms…

Jens Rittscher (University of Oxford, UK)
Florian Jug (CSBD / MPI-CBG)
Anna Kreshuk (HCI, University Heidelberg / EMBL)

[NEUBIAS] Machine Learning Workshop/course at EMBL, Oct 29-31.

Dear MC Members/Substitutes/Observers,

It is our pleasure to advertize the following Workshop/Course organized by EMBL, and jointly organised/funded by CORBEL, EMBL, German BioImaging and NEUBIAS.

This is a blended learning course on Machine Learning for Image Analysis, consisting of three online sessions with associated hands-on exercises prior to the workshop, a three day face-to-face workshop at EMBL Heidelberg and two optional online sessions with associated hands-on exercises after the workshop. 

This course is unique and pioneering, and from NEUBIAS we think it will set an example/path on how to integrate Machine learning and Deep Learning for further Teaching/Training events.

The course is free of charge but subject to selection.
and I ask all MC members to please advertise this around them,
NEUBIAS will provide 4 travel grants
as agreed and voted in the Grant Period 3 Budget & Workplan.

The prior condition to be eligible for those travel grants is: apply and be selected to participate in the course by the organizers.
A 2nd step will consider the successful candidates that have applied to a grant, and a NEUBIAS selection committee composed of three experts in machine learning will select 4 successful candidates, based on motivations and the application of COST policies.
We look forward to see many applications to this innovative workshop/course.

Best greetings,


Julien Colombelli
Head of the Advanced Digital Microscopy Core Facility
Institute for Research in Biomedicine – IRB Barcelona
Barcelona Institute of Science and Technology – BIST
Baldiri Reixac, 10.
E-08028 Barcelona – Spain
Tel:  +349340-20451   —   Fax: +34934031116

Network of European Bioimage Analysts – NEUBIAS
Chair  – COST Action CA15124