Congratulations Dr. Preusser!

Great defense, I’m very happy we could do this in person at the BIMSB / @MDC_Berlin 😊

Why do airlines think that leaving the lights on in an overnight flight is a good idea? I really don't get it ... especially now that I travel with kids, but also before actually ...

It was a pleasure to host Loic Royer (CZI Biohub) for a Napari-ChatGPT Code Review @hhmijanelia

It was very exciting and I think watching it will give you a nice introduction to the project, but also how to get started using the API for your own projects:

youtube.com/watch?v=JMo6Sn-L_j

The Scientific Computing group at #HHMIJanelia seeks a software engineer, to work on large-scale electron #microscopy reconstruction and analysis. Come work at the forefront of #imaging and #OpenScience with applications in #Neuroscience and #CellBiology. Janelia welcomes and values diversity, and encourages applications from people of all backgrounds, including people of color and members of groups traditionally underrepresented in science. (#FediHire, #FediHired)

hhmi.wd1.myworkdayjobs.com/en-

Scientific Computing Software Engineer

Primary Work Address: 19700 Helix Drive, Ashburn, VA, 20147 Current HHMI Employees, click here to apply via your Workday account. Position Summary We are looking for a software engineer with expertise in mathematics to work in the Scientific Computing Department on exciting projects that involve large data volume electron microscopy reconstruction and analysis. You will work with laboratories and team projects at HHMI Janelia to develop scalable software for imaging data produced at Janelia. Initially, the focus of the position will be streamlining and expanding existing tools for the alignment of multi-terabyte-sized electron microscopy acquisitions produced by the FIB-SEM (Focused Ion Beam Scanning Electron Microscopy) core at HHMI Janelia. This includes development of Java code for distributed non-rigid image alignment, quality control, and workflow optimization using established open-source libraries ImgLib2, BigDataViewer, N5, and Spark. The candidate will have the opportunity to contribute to efforts for robustly aligning peta-scale MultiSEM datasets currently produced by the Hess lab. Based on these experiences you will have opportunities to take on new interesting projects with different teams and/or labs at HHMI Janelia that will also provide the opportunity for professional development, for example in the domain of machine learning. HHMI Janelia recently started its new research direction “4D Cellular Physiology”, which will produce plenty of exciting computational challenges and opportunities. The Scientific Computing Software department at HHMI Janelia is an exciting environment where you will have the opportunity to collaborate with excellent software engineers and scientists and have access to the latest and most exciting data and computational resources. Education: Ph.D. or M.S. in Computer Science or related field Experience: Experience with writing efficient code with Java or other JVM based languages Experience with mathematics, specifically linear algebra Ideally experience with libraries such as Spark, ImgLib2, N5, BigDataViewer Familiarity with Python, other programming languages Ideally, you have a record contributing to open-source projects, so we can discuss code If you do not meet all of the above criteria but you are convinced that you can compensate this with enthusiasm, creativity, and practical experience, reach out to us and let's talk. For more information on Scientific Computing at HHMI Janelia, visit here or email People & Culture at (email) or Stephan Preibisch at preibischs@janelia.hhmi.org directly. Compensation Range Software Engineer III: $113,190.00 (minimum) - $141,400.00 (midpoint) - $183,810.00 (maximum) Software Engineer IV: $131,818.40 (minimum) - $164,773.00 (midpoint) - $214,204.90 (maximum) Pay Type: Annual HHMI’s salary structure is developed based on relevant job market data. HHMI considers a candidate's education, previous experiences, knowledge, skills and abilities, as well as internal equity when making job offers. Typically, a new hire for this position in this location is compensated between the minimum and the midpoint of the salary range. Compensation and Benefits Our employees are compensated from a total rewards perspective in many ways for their contributions to our mission, including competitive pay, exceptional health benefits, retirement plans, time off, and a range of recognition and wellness programs. Visit our Benefits at HHMI site to learn more. HHMI is an Equal Opportunity Employer Howard Hughes Medical Institute (HHMI) is an independent, ever-evolving philanthropy that supports basic biomedical scientists and educators with the potential for transformative impact. We make long-term investments in people, not just projects, because we believe in the power of individuals to make breakthroughs over time. Why HHMI To move science forward we need a diverse collection of talents, expertise, and backgrounds in scientific research and science education, as well as communications, finance, human resources, information technology, investments, law, and operations. At HHMI, we encourage collaborative and results-driven working styles and offer an adaptable environment where employees can do their best work. What makes us strong is the diversity of our perspectives. We work to promote a culture of inclusion in our work environments and across the greater scientific community. To find more information about us and the steps we're taking to make HHMI a more inclusive organization, visit our About Us page. A Note for Job Seekers Your best option for consideration in our career opportunities is to apply directly via our HHMI Careers site. There, you will learn more about HHMI and can find information about our available roles. Contact us at recruitingsupport@hhmi.org if you require an accommodation related to completing the job application. All information you provide will be kept confidential and will be used only to the extent required to provide needed reasonable accommodations.

hhmi.wd1.myworkdayjobs.com

We are looking for a software engineer with background in mathematics and/or image alignment to work with us on reconstructing very large electron microscopy volumes:

hhmi.wd1.myworkdayjobs.com/en-

Today the peer-reviewed version of our preprint is out:

"The #connectome of an insect brain"
science.org/doi/10.1126/scienc

Congrats to co-first authors Michael Winding and Benjamin Pedigo, and to all our lab members and collaborators who made this work possible over the years. A journey that started over 10 years ago–and yet this is but a new beginning. So much more to come.

See my #tootprint on the preprint from back in the Autumn: mathstodon.xyz/@albertcardona/

The data is available both as supplements and directly via #CATMAID thanks to hosting by the #VirtualFlyBrain:
l1em.catmaid.virtualflybrain.o)

(The "Winding, Pedigo et al. 2023" annotation listing all included neurons will appear very soon in an upcoming update.)

#neuroscience #connectomics #Drosophila #DrosophilaLarva

Latest report from the #OMENGFF #Community describing #OMEZARR, a #CloudOptimized #BioImaging #DataFormat, is out now on #bioRxiv!

If you are having trouble with big, slow, or otherwise unwieldy imaging data, reach out or take a look for a #FAIR-er option.

biorxiv.org/content/10.1101/20

We have an open #postdoc position in #RNA biology. Combine Genomics and proteomics to develop new tools to explore RNA protein interactions. A collaboration with Ilaria Piazza’s lab (MDC Berlin). Come and join us in #Stockholm SciLifeLab Karolinska Institute Deadline 30 Jan. pelechanolab.com/2023/01/11/po

Follow-up update for is out! Now supports:
1) export of BigDataViewer/BigStitcher compatible HDF5/N5 datasets
2) export of datasets for 2D images and 2D slices of 3D images

Stephan Preibisch  
Exciting New Year's release of #BigStitcher! It now supports: 1) efficient blocked processing, meaning large, tiled acquisitions are fused blazing...

Exciting New Year's release of ! It now supports:

1) efficient blocked processing, meaning large, tiled acquisitions are fused blazingly fast (second/minutes instead of hours)!

2) Export of ZARR/N5/HDF5 thanks to the N5-API

Check it out, just update Fiji!

Hi everyone, does anyone know current approaches for segmenting organs of known, annotated shape in low resolution modalities such as ultrasound?

We need it for similar problems in biology and microscopy ...

Thanks so much!!

@preibischs interesting experiment which shows, not surprisingly, how the outcome can be biased by the training set. Most of those recipes are quite South German, Bavaria and the Black Forrest area. The type one would see in a American movie depicting German stereotypes.

I do think AI as an enormous potential but I think it's easy to ignore the errors which are only detect by human experts in a particular field.

I got curious about and the associated questions related to ownership - so I quickly created a with outstanding recipes by asking questions and DALL-E to generate images ... check it out

drive.google.com/file/d/17DXeT

Which license does code have that creates? Can I use it and license as anything I want? itself did not answer the question ...

We are looking for a Technical Assistant in the research lab of Jacqueline Tabler at the MPI-CBG. The Tabler lab investigates the cellular and biophysical mechanisms governing morphogenesis and cell fate in the embryonic mouse skull. Apply here: mpi-cbg.de/join-us/open-positi

Mastodon gets un-suspended and then goes for the posterizing dunk right out of the gate #tech #socialmedia

For those who still have a Twitter account, you might want to vote on this one

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