Once again, we bring you HuBMAP's Image of the week! This week has two images, both from Liz McDonough at GE Research. The top image is Cell DIVE, and maps proteins in order to see the damage done by the sun to the epidermis, surrounded by immune cells and blood vessels. The image on the bottom is a different imaging technique (H&E) of the same region. Remember to always wear your sunscreen!
Are you looking for fame and notoriety? Send your best images to dena.procaccini@nih.gov.
Evaluation of Image Analysis Methods for Cell Segmentation
The HIVE Computational Tools component is conducting an evaluation of image analysis
methods for cell segmentation for use in HuBMAP pipelines. We would like to include all
current methods in the evaluation, so if you are using or know of relevant software we would
encourage you to let us know about it. In order to be included, the software should:
be available as open source software that runs under linux and does not require any commercial licenses
include a pre-trained model(s) that is applicable to 2D or 3D microscope images
produce a cell boundary segmentation from input images of one or more of the
following markers
Nucleus
Cytoplasm
Cell membrane
not require any additional input beyond acquisition metadata, such as pixel size, for the input images (i.e., should not require any tuning parameters)
If you have any suggestions, please send the URL for the software to murphy@cmu.edu. All
results will be made publicly available.
Consortium Publications
The C3P Working Group is requesting that each funded group review and update the publications tracker for recent publications, both planned and published. Note that the tracker now includes a new column that will need to be completed for each publication: Consortium Package[yes/no]
Please finalize your edits no later than 1/18/2021. The C3P WG will be reviewing the tracker updates at their meeting on 1/19/2021.
Postdoc Opening - TTD UCSD
The Zhong lab at USCD is actively recruiting postdoc scholars to innovate in RNA biology and technologies, including spatial, single-cell, and extracellular transcriptomics.
Summer undergrad internships are now open (deadline January 21). More information here.
A new paper is out in eLife on cell class nomenclature, a convention applicable to any organ with a taxonomy. Link to paper here.
HCA Bionetworks Seminars
The Human Cell Atlas is launching a series Bionetwork Seminars with the first one scheduled for this Thursday, January 14 from 10:30 - Noon (EST) focusing on Breast and Liver networks.
HuBMAP researchers are encouraged to join and participate. Link to more information here. For late registration, contact Ellen Todres here.
Job Posting
Pacific Northwest National Laboratory
The Environmental Molecular Sciences Division at Pacific Northwest National Laboratory (PNNL) seeks for an outstanding candidate for a postdoctoral position working on projects associated with biological applications of high throughput and quantitative proteome mapping of tissue heterogeneity of the pancreas at near single-cell resolution.
Underrepresented/Minority Internship Program (HuBMAP)
The HuBMAP Minority Internship Program is now accepting applications through February 15th.
Please help us get the word out by distributing this opportunity to any students or colleagues that my have interested students. This virtual internship program provides a fantastic opportunity to build connections, add to your experience and conduct vital research in the single cell community.
Check out the newly released video, produced by HuBMAP associate member Mark Musen, that provides an introduction to ontologies - what they are, how they're used and why they're important in BioMed applications (for HuBMAP in particular). Link to the video here.
RFAs/Labs/Competitions
HeartShare: Next-Generation Phenomics to Define Heart Failure Subtypes and Treatment Targets (RFA)
Developers in need of HIVE infrastructure may request access through the PSC web form, found here.
Instructions for using HIVE infrastructure can now be found in the "Quick Links" section of the Collaboration Portal. A direct link to this documentation can be foundhere. Please report any issues or direct any questions tohelp@hubmapconsortium.org.
Content Suggestions
The IEC is seeking to collect information of general interest from individual members and groups to share with the rest of the Consortium. Please submit content suggestions by emailing: admin@hubmapconsortium.org.
Past Newsletters are available on the Collaboration Portal.
For comments, suggestions about how to improve the HuBMAP Happenings, or questions about the consortium, please contact: help@hubmapconsortium.org
