Anyone feeling like working in Singapore? Here is your chance! 😁
Tomorrow (17 sept) we will enjoy a seminar and a live demo about the Crest V3 spinning disk confocal which is being set up at our facility as I write! 😀
Very cool confocal!
- enormous field of view (32 mm diameter)
- fully confocal
- can image at 100 frames per sec
- spits out Nyquist resolution with the 60x objective!
You can come to the seminar (at 10 in the Gene seminar room at the LCI facility) or listen to it remotely (see here how to follow the LCI webinars).
You can even book a private demo to image your own samples.
To image a thick sample, it is crucial to match the refraction index of the sample with that of the immersion medium between the sample and the objective. Typically, life samples are in an aqueous solution like culture medium which has a refraction index of 1.33. Unfortunately organoids often have a higher refraction index closer to 1.44 therefore as one images deeper into the organoids, light scatters due to the refraction index mismatch and the images become blurry.
This paper presents a product that has a high RI and is compatible with cell culture. Good to keep in mind for those who image organoids over time.
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! 😀
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:
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.
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
In the UK
I am looking for a junior scientist to develop light sheet microscopy in combination with probes to monitor cell signalling in 3D cultures, optogenetics to seed cancer causing mutations and modelling techniques to study events in early steps in oncogenesis. The project is highly interdisciplinary but I would like to find someone who is strong on the microscopy developments. The advert is published at the following link: https://www.jobs.cam.ac.uk/job/22329/ And a general description of the project here: https://oncolive.online/ Cheers, Alessandro MRC Cancer Unit, University of Cambridge Hutchison/MRC Research Centre Box 197, Biomedical Campus Cambridge, United Kingdom CB2 0XZ https://quantitative-biology.org
Two Research Managers in Biological and Medical Imaging for a fixed period employment at Turku Bioimaging. Our organization Turku Bioimaging is a research organization to employ and promote the strengths of both biological and medical imaging in the Turku region. The organization was established in 2007 and now University of Turku and Åbo Akademi University have agreed to reinforce Turku Bioimaging by strategic recruitments. The organization and its team are internationally renowned with many important national and international tasks related to coordination and promotion of imaging science. Please read more about us here: https://www.bioimaging.fi/ We are now looking for two talented persons for the positions of Research Manager. One of them will be for the field of Medical Imaging with the base location at Turku PET Centre. The other will be for the field of Biological Imaging with the base location at Turku Bioscience. https://bioscience.fi/ Positions are for a fixed period of one year, with a likely continuation for a 2-years-prolongation. After three years, the positions will be evaluated for a possible long-term continuation. Starting date is October 1, 2019 and there is a trial period of six months. Job description The task of the Research Manager is to support the research activities in the field of Biological/Medical Imaging within the Turku Bioimaging. The responsibilities will involve participation in the application processes and preparing applications especially for different EU funding opportunities. The tasks will also involve strengthening the roles of Turku Bioimaging in Euro-Bioimaging status as well reinforcing the position of Turku Bioimaging in Finnish roadmap for research infrastructures. The tasks will also include national coordination of the research within Biological/Medical Imaging. What we are expecting from you Success in the position requires a broad knowledge of techniques and concepts in Biological/Medical Imaging, including practical and theoretical understanding on how to conduct scientific research. A successful applicant should preferably also have experience in preparation, coordination, management, and reporting of research projects. As the core task for the Research Manager is related to funding, understanding of research infrastructures and how they operate (at both national and international levels) is considered important, as well as a thorough understanding of especially EU-level funding opportunities. Finally, insight into image data management is considered an advantage. A doctoral degree in an appropriate field is required and a Docentship (adjunct professorship) in an appropriate field is considered also an advantage. The Research Manager is also required to have a good written and spoken English and readiness to travel and to represent Turku Bioimaging at national and international meetings. You also need good interpersonal skills and ability to communicate and collaborate with scientists and industrial partners from many different disciplines. Salary and application The salary is determined by the collective agreement system of Finnish universities. The Research Manager belongs to our research personnel and salary will be 4183 – 4500 eur/month in average. Please write a CV and a motivation letter that describes why you are applying for the position and how you would like to develop Turku Bioimaging and bioimaging in general in Turku. In the motivation letter, please also describe your vision of how Turku Bioimaging should be developed in terms of Biological and Medical Imaging and how the collaboration of relevant imaging scientists and centers in Finland and in Europe should be developed in the future. Please submit your application by using our electronic application: https://www.utu.fi/en/university/come-work-with-us/open-vacancies Application deadline is September 1st, 16:00. We will read the applications already during the application process, so please send your application at your earliest convenience. In case you need help in the application process, please don’t hesitate to contact our HR Specialist Paula Luoma email@example.com. Director, Professor John Eriksson, Turku Bioscience, tel. +358 2 215 3313, firstname.lastname@example.org Director, Professor Juhani Knuuti, Turku PET Centre, tel. + 358 500 592 998, email@example.com
and in Switzerland
Image analysis specialist / software developer (80-100%) Starting 1 October 2019 or as per agreement The Biozentrum of the University of Basel is one of the leading life sciences institutes in the world. It consists of 32 groups and 500 employees that research how molecules and cells create life, spanning the scale from atom to organism. Founded in 1971, the Biozentrum has been the birthplace of many fundamental discoveries in biology and medicine, spawning several Nobel Laureates. The Imaging Core Facility (IMCF) is a well-established technology platform at the Biozentrum offering access to high-end microscopy systems and highly sophisticated image processing IT infrastructure. The biological applications cover research areas including cellular biochemistry, cell biology, microbiology, infection biology, neurobiology and developmental biology. The IMCF is looking for a junior image analysis specialist / software developer with a strong interest in biological applications. As an ideal candidate, you should be service-minded, proactive, and a good team player. You will be part of a team of experts designing, implementing and evaluating new software solutions for image analysis to support Biozentrum scientists in their research projects. Your responsibilities Typical tasks include:
Scripting for data management tasks
Development and implementation of image / data processing pipelines, mostly based on common bio-medical toolkits like ImageJ/Fiji, CellProfiler, QuPath, Ilastik etc.
User training and support with image analysis related topics
Many of these tasks will be done in close collaboration with our colleagues of the Research IT facility. Your profile We are looking for an enthusiastic person with a Master or PhD degree in Computer Science, Physics, Biology or a related field, who has proven competence in image processing and development of user-friendly software using Python, Java, Groovy and/or ImageJ-Macro. As an ideal candidate, you should be service-minded, proactive, and a good team player. We collaborate with imaging facilities and staff scientists in-house and across Switzerland, and expect you to have excellent social and networking skills and to enjoy collaborating with peers. Good communication skills in English are essential. We offer The Biozentrum offers a cutting-edge research infrastructure, a highly international environment, and excellent working conditions. The position is initially limited to 12 months but might be prolongated to up to 5 years. Salary and benefits according to University of Basel standards. Application / Contact Please apply online by 15 September 2019 with a CV, letter of motivation, and the name/address of three references: https://biped2.biozentrum.unibas.ch/apply/image-analysis-specialist Please note that only online-applications will be accepted. For further information, please feel free to contact Oliver Biehlmaier, PhD, Head of Imaging Core Facility (firstname.lastname@example.org<mailto:email@example.com>, +41 61 207 20 73)
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! 🙂
Hans Blom and the Advanced Light Microscopy facility at Scilife organise one of their great super resolution microscopy course and a bunch of great seminars in September.
More information about the course and the seminar program (26th of september) can be found here.
See you all there! 😀
BIC, the imaging facility at KI on the Solna campus, organises a Zeiss workshop at the end of August. Contact them if you want to participate. 🙂