BIIF Newsletter, January 2022

BIIF logo

New BIIF members

We are happy to announce that Saga Helgadóttir and Robert Welch joined BIIF with the start of the new year.
Saga has a background in data analysis and visualization. She defended her PhD thesis at GU in 2021, which was about developing tools using deep learning to solve problems in image analysis and medical diagnosis. Saga is also interested in high-throughput image processing, and will be focusing on in situ sequencing, making data handling, pre-processing and analysis better and faster. Her work will contribute to the new SciLifeLab capabilities in spatial omics.
Rob has a background in image and signal processing. He recently defended his MASc thesis from the University of Toronto, which focused on developing novel photothermal imaging algorithms for biomedical applications. His other interests include any outdoor activities or sporting events.

Welcome Saga and Rob!

Saga and Rob

Call4Help

The next Call4Help session is coming up on February 11, 2 – 4 pm, information here. Note that you can always contact us under biif@scilifelab.se to set-up a meeting and receive support on image analysis. The idea of the Call4Help session is to provide combined support on both the image analysis and the microscopy part of a project.

Upcoming Webinars

LCI course - Microscopy: improve your imaging skills - from sample preparation to image analysis

The Live Cell Imaging core facility at the Karolinska Institute in Sweden will starts its intensive microscopy course today - January 24th. Applications are closed but all lectures are broadcasted live and open to anyone without registration.

More information: https://ki.se/en/bionut/lci-microscopy-course/

NEUBIAS Academy webinar on CellPose

Cellpose is a deep-learning based tool for whole cell segmentation, which comes with generalized pretrained models. It works very well for whole cell, nuclei and tissue sections (imaged using fluorescence, phase contrast or DIC methods) without the need to do any additional preprocessing and model training. There are different implementations of cellpose including a web-based interface, ZeroCostDeepLearning4Mic, jupyter notebook, Fiji, Napari, QuPath and CellProfiler-based platforms. During the webinar we demonstrate how cellpose works and how one can run it on their own datasets.
Presenter: Carsen Stringer (HHMI, Janelia, USA)
Date: 25 January 2022, 15h30 – 17h00

Apply for NBIS Bioinformatics Long-term Support

The Bioinformatics Long-term Support offers extensive bioinformatics support to a limited set of scientifically outstanding projects. This support has been enabled primarily by a generous grant from Knut and Alice Wallenberg Foundation (KAW). The idea is simple: A senior bioinformatician will work in your project 500 hours for free. Deadline: 28 January 2022

Best regards
Anna, in behalf of BIIF