CellMorphoSero . bsky . social retweeted
We look forward to this Friday's #VirtualPub with @joel_luethi, Friedrich Miescher Institute for Biomedical Research, and Bugra Özdemir of Euro-BioImaging. They will take us on an "Exploration and Analysis of Image Data using #OMEZarr."
All are welcome! ⤵️
eurobioimaging.eu/about-us/v…
CellMorphoSero . bsky . social retweeted
Teresa Zulueta-Coarasa, @microRussell & Matthew Hartley present @emblebi's contribution to AI4Life: standardization of AI-ready datasets to be stored in the @BioimageA. The manuscript is in preparation but here's a sneak peek: ai4life.eurobioimaging.eu/su…
CellMorphoSero . bsky . social retweeted
Straight on the back of the excellent talks at #LABIxBINA2023 Beth Cimini stars in #TheMicroscopists (@broadinstitute) and discusses the challenges of developing popular software tools like #CellProfiler in academia and why harsh peer reviewing is your friend and leads to better user-friendly software. Plus - why someone on X (formerly Twitter) got mad when Beth shared a picture of pasta.
See/Hear: bit.ly/microscopists68-pt
#DataScience #Microscopy
CellMorphoSero . bsky . social retweeted
Hey, if you are on the bsky social can you like this post? I'm trying to migrate over there in case this climate gets too unclement.
CellMorphoSero . bsky . social retweeted
Choudhury, M. I., Li, Y., Mistriotis, P., Vasconcelos, A. C. N., Dixon, E. E., ..., Konstantopoulos, K., Woodward, O. M., & Sun, S. X. (2022). Kidney epithelial cells are active mechano-biological fluid pumps. Nature Communications
#EpithelialMechanics
doi.org/10.1038/s41467-022-2…
CellMorphoSero . bsky . social retweeted
Great to hear from @jennypowerhour about her work on modelling radiotherapy with mathematics @UniofBath @Cancer_at_Bath @LifeScienceBath @UniofBathSci @RUHBath
CellMorphoSero . bsky . social retweeted
The PhD program of the @mpicbg, the @imprs_mpicbg, is accepting applications until October 30, 2023 for fully funded PhD positions. Apply now if you are enthusiastic in conducting research with us and want to be part of our community. digsbb-online-application.cm…
CellMorphoSero . bsky . social retweeted
JCB is pleased to present a special collection highlighting recent papers on the mechanical properties of cells and tissues, and the application & transmission of forces across scales relevant to cell biology. Gain new insights into #mechanobiology 👉 bit.ly/3sMxtF9
CellMorphoSero . bsky . social retweeted
Dynamic nature of the nuclear envelope (NE) wrinkling is beautifully shown in this time-lapse video recorded by Jackson et al. They mathematically explain how similar the NE and..plain paper, much like they are both prone to bend than to strech. Read it at rdcu.be/dmCch
CellMorphoSero . bsky . social retweeted
#Derna Valley
Its length exceeds 70 kilometers, and it extends southwest of Derna to empty into the Mediterranean Sea. It has 3 parts, the first with an area of 345 square kilometers, the second part with an area of approximately 140 square kilometers,1/3
#Libya
CellMorphoSero . bsky . social retweeted
Utter devastation as Medicane Daniel strikes Cyrenaica/Eastern Libya 🇱🇾 😔 1000s are lost or have lost their lives following floodings in Derna, Al-Marj, Al-Bayda and Benghazi. Entire neighbourhoods are completely inaccessible with no form of communication, in dire need of aid
This quoted post is unavailable.
CellMorphoSero . bsky . social retweeted
You need a cheat sheet to effectively get from microscope image to publication-ready figure? You may like the poster summaries @ChriSchmied and I made.
Fun fact, we used as template of the great @posit_pbc @rstudiotips cheat sheets 😁
blog 7: helenajamborwrites.netlify.a…
CellMorphoSero . bsky . social retweeted
We wrote a perspective on "Machine learning enhanced cell tracking". Huge thanks to @jytinevez and Ko Sugawara for excellent feedback during review!
frontiersin.org/articles/10.…
#MachineLearning #imagingthefuture #bioimageanalysis
CellMorphoSero . bsky . social retweeted
Our latest #preprint list is now available. This week we focus on new research in #bioimageanalysis, including a number of methods using generative AI. Let us know if we have missed any recent preprints and we’ll add them to our list.
focalplane.biologists.com/20…
CellMorphoSero . bsky . social retweeted
Cells from a fish crawling on a piece of glass videoed through a microscope. They were alone and then together. #CellBiology
CellMorphoSero . bsky . social retweeted
We discovered a surprisingly easy way to control the brightness of fluorescent proteins via magnetic fields:
andrewgyork.github.io/gfp_ma…
This raises fascinating scientific questions about the mechanism, and tantalizing technological opportunities for bioengineering.
CellMorphoSero . bsky . social retweeted
Check out our new paper by the extremely talented postdoc @James__Cornwell out now in @Nature. For decades it was thought the cell cycle was irreversible, but now we show that is not the case.
nature.com/articles/s41586-0…
CellMorphoSero . bsky . social retweeted
🎉Exciting Update of scGPT 🎉: After receiving significant attention from the community since our April release, we're thrilled to announce the first major update for scGPT - a foundation model for single-cell multi-omic data.
This update integrates community feedback and leverages the latest data release from @cellxgene. It boasts larger pretraining data, and more robust models, and expands the range of application tasks.
Pre-print (V2) available: biorxiv.org/content/10.1101/…
Access our open-source code and models here: github.com/bowang-lab/scGPT
Detailed tutorials: scgpt.readthedocs.io/en/late…
Highlights of this update include:
🔬 Introducing the first GPT-style foundation model for single-cell multi-omic data, pretrained on over 33M human cell atlas data.
💡 Our generalist approach enables one model to accomplish multiple tasks in single-cell analysis, including multi-omic integrative analysis and perturbation prediction.
🧬 Discovering gene-gene interactions specific to various conditions using learned attention weights and gene embeddings.
🚀 Uncovered a scaling law showcasing continuous model performance enhancement as data volume increases.
🐾 scGPT model zoo (see github) now offers multiple pre-trained foundation models for various solid organs and a comprehensive pan-cancer model. Begin exploring your data with the most fitting foundation model.
We welcome your thoughts on specialist vs generalist approaches in single-cell studies. Many thanks for the following technical analyses of scGPT:
1. Excellent twittorial by @simocristea: xitter.cf/simocristea/stat…
2. Comprehensive review on LLM in cell biology by @s_batzoglou: towardsdatascience.com/large…
3. Insightful blog by @SalvatoreRaieli: levelup.gitconnected.com/scg…
Kudos to Haotian (@HAOTIANCUI1) & Chloe (@chloexwang1) for their exemplary work on this project. @VectorInst @pmcc_ai @UHNAIHUB @bradwouters @drbarryrubin @UofT_TCAIREM @UofT_LMP @UofTCompSci @uoftmedicine
CellMorphoSero . bsky . social retweeted
A mind-blowing paper has come out today in @Nature
In 2016, JC Venter Institute scientists trimmed a bacterial genome to its barest minimum required for life to synthesize what they called a "minimal genome" (science.org/doi/10.1126/scie…).
Today, a group of scientists from Indiana University reports how that minimal genome evolved over 2000 generations in comparison to the non-minimal genome.
The authors found that even when you reduce a bacterial genome to its absolute minimum where every nucleotide matters, the genome undergoes mutational events generation after generation as much as the non-minimal genome. One simply cannot stop the evolution.
Just over 300 days of evolution (equivalent to 40,000 years in humans) the minimal cell has gained everything it lacked in fitness on day one in comparison to the non-minimal cell.
When comparing the evolved traits between the minimal and non-minimal cells, the scientists found something striking. The evolutionary process increased the cell size of non-minimal cells but not that of the minimal cell. But that is not the striking part.
The scientists were able to identify the key mutation that resulted in cell size evolution. And it turned out that the mutation that helped the non-minimal cells to grow bigger is the same that helped the minimal cells to stay smaller. Growing bigger had a survival advantage for non-minimal cells and not growing bigger had a survival advantage for minimal cells. So, the mutation had a context-dependent effect. This just demonstrates that the evolutionary effects on traits have no absolute direction. All that matter is what is beneficial for the organism's survival.
The conclusion of the paper is metaphorically a quote from the Jurassic Park movie:
“Listen, if there’s one thing the history of evolution has taught us is that life will not be contained. Life breaks free. It expands to new territories, and it crashes through barriers painfully, maybe even dangerously, but . . . life finds a way". (scienmag.com/artificial-cell…)
nature.com/articles/s41586-0…
CellMorphoSero . bsky . social retweeted
😲 Time to revise textbooks 🤔
Title: "Transcription factors interact with RNA to regulate genes"
"at least half of TFs also bind RNA, doing so through a previously unrecognized domain"
cell.com/molecular-cell/pdf/…
































