Sam Lord
@samjlord.bsky.social
Cell biology and microscopy researcher in the @MullinsLab at UCSF. I publish as Samuel J. Lord. https://blog.everydayscientist.com/
I created a simple ImageJ/Fiji button that toggles the LUT between gamma = 0.45 and 1. The goal is to correct microscopy images for the nonlinear gamma of computer monitors, but do to without changing the underlying pixel values. github.com/samjlord/Gam...
A simple template to help with experimental planning and preregistration. Any suggestions for edits/additions? blog.everydayscientist.com/the-case-for...
I made a visual sample size calculator to help use our intuitions about how our graphs typically look to estimate the effect size and the required sample size. I'm looking for input to make it more useful. Or if you spot bugs. samjlord.shinyapps.io/visualsample...
Update: our #PeerReplication idea is now published in EMBO Reports: doi.org/10.1038/s443...
Peer replication - EMBO Reports
EMBO Reports - To address the replication crisis and instill confidence in the scientific literature, we introduce a new framework for evaluating scientific manuscripts. “Peer...
doi.org
Sam Lord@samjlord.bsky.social · 3y agoWe're seeking feedback on our white paper on PeerReplication. Arthur, Kristen, Dyche, Anders, and I propose an alternative or augmentation to peer review, where key experiments are reproduced, adding robustness to published findings. zenodo.org/doi/10.5281/...
#arXiv #April1st PromoPlot: Covering open-access fees by filling wasted space in corner plots https://arxiv.org/abs/2503.24254 a novel technique can allow authors to reduce or eliminate publication charges for journals such as MNRAS and ApJ.
Here's the reason I ask: I'd like to write up about some basic science researchers who preregistered their plan and how the experience ultimately played out. #OpenScience #Preregistration blog.everydayscientist.com/the-case-for...
Everyday Scientist » The Case for Preregistration in Cell Biology: A Practical Guide
blog.everydayscientist.com
Sam Lord@samjlord.bsky.social · 7mo agoAny cell biologists out there who have preregistered your data collection/analysis plans before starting an experiment? Either on an official depository or unofficially? I'd be curious about your experience.
Any cell biologists out there who have preregistered your data collection/analysis plans before starting an experiment? Either on an official depository or unofficially? I'd be curious about your experience.
Here's my idea for better science funding: blog.everydayscientist.com/end-grant-wr... Instead of funding grants, just award financial prizes for good papers. Award half the prize upon publication; award the second half upon replication, 25% to the original authors and 25% to the replicators.
Everyday Scientist » end grant writing; award prizes for papers instead
blog.everydayscientist.com
Preprint drop! 🚨 Rhobin-tag your proteins and watch Saci glow at high temps! 🔥 Bright, photostable, live-cell imaging made possible with JF dyes. Huge thanks to @samjlord.bsky.social @acharlesorszag.bsky.social @mullinslab.bsky.social and Bo Huang lab at UCSF.😊 www.biorxiv.org/content/10.1...
De novo designed bright, hyperstable rhodamine binders for fluorescence microscopy
De novo protein design has emerged as a powerful strategy with the promise to create new tools. The practical performance of designed fluorophore binders, however, has remained far from meeting fluore...
biorxiv.org
So grateful to all collaborators on this huge effort! @mullinslab.bsky.social at UCSF with Natalie Petek, @samjlord.bsky.social, and @skruberk.bsky.social now at Gonzaga with Ethan MacVicar for microscopy & motility analyses
The Incindiamoeba preprint is out and getting great press! (featuring one of Natalie Petek's HOTTT movies) Congratulations to Beryl Rappaport (@hbrappap.bsky.social) and everyone else who made this happen (including @samjlord.bsky.social and @skruberk.bsky.social). Super-fun collaboration!
‘Fire amoeba’ survives in hotter conditions than any other complex cell
The single-celled organism can grow at 63 °C, a record for eukaryotic life.
nature.com
Preprint alert! I’m publishing my last paper from my postdoc work on archaeal cell biology, with @mullinslab.bsky.social, @archaellum.bsky.social, @samjlord.bsky.social, @marleenvw.bsky.social, @arghya93.bsky.social, and more great folks (thread below with more details)
bioRxiv Cell Biology@biorxiv-cellbio.bsky.social · last yr.Archaeal SegAB forms a bipolar structure that promotes chromosome segregation in spherical cells https://www.biorxiv.org/content/10.1101/2025.04.15.649018v1
New actin probe from @veselin-nasufovic.bsky.social et al! SiR-XActin and its variants are more photostable and less perturbative than SiR-actin or FastAct. And it's already available from @spirochrome.com! With some beautiful data from @chillinwithpfn1.bsky.social: www.biorxiv.org/content/10.1...
Calling all Bay Area researchers for a paid opportunity: the @asterainstitute.bsky.social Open Science Program’s User Testing Day in Emeryville on Feb 11! 📍 Try cutting-edge research tools 💡 Share feedback 🍷 Network Apply by Feb 5: forms.gle/1qk4PHjbee35... #UXTesting #Biotech #OpenScience
Application to the Astera Open Science program's user testing day
Are you a Bay Area researcher in academia or industry? Do you want to make an impact on innovative tools designed to transform the way we work and think? Apply below to be a part of the Astera Open Sc...
forms.gle
How can the dose be an order of magnitude lower than they first estimated, but then have zero change in their conclusion? Shouldn’t their concern about black plastic cookware be 10x lower now?? www.sciencedirect.com/science/arti...
The Study That Called Out Black Plastic Utensils Had a Major Math Error — WIRED
Despite the correction, the study’s authors stand by their conclusions about the risks of certain kitchen utensils.
apple.news
“NIH reiterates that compliance with the Policy does not require the payment of an open access fee to a journal…free pathway to compliance can be achieved by depositing the Author Accepted Manuscript into PubMed Central for public availability upon the Official Date of Publication without embargo.“
Prachee Avasthi@pracheeac.bsky.social · 2y agoHot off the presses today is the 2024 NIH Public Access Policy. I read it so you don’t have t…Just kidding. You should still read it in full if you do NIH funded research. grants.nih.gov/grants/guide... Some highlights in the thread below
Advances in microscopy mean we can now do more than just observe biology—we can control it. But how far can we really push this in mammalian cells with all their (beautiful but annoying) heterogeneity? 🧪🔬(🧵)
Speakers, try adjusting gamma on your images (e.g. 0.45) on your slides. Especially for images that are still hard to see after optimizing contrast. #CellBio2024
Sharing my latest preprint as a re-introduction to bsky! biorxiv.org/content/10.1... ---- Everyday, cells like this crawl through your body to protect you. While we know that their front 🔴 and back 🔵 polarity programs work together, how exactly do these two processes communicate?
I love SuperPlots! If I can shamelessly share an article I wrote this year about some do's and don'ts of data viz, I also included a reproduction of the same figures of the paper in Python here: pub.ista.ac.at/~mdallave/re...
Dos and Don’ts of data visualization
pub.ista.ac.at
Q: What's wrong with these plots? A: Pooling cell-level measurements across multiple runs conceals experimental reproducibility. Read more in JCB (with @fritzlaylin.bsky.social @katrinavelle.bsky.social & Dyche Mullins): rupress.org/jcb/article/...
A starter pack of starter packs...
Razvan Borza@rborza.bsky.social · 2y ago⚠️THREAD OF ALL SCIENCE-RELATED STARTER PACKS! ⚠️ 🔄Share to help people finding its topic/field - STRUCTURAL BIOLOGY Structural Biology 1: bsky.app/starter-pack... Structural Biology 2: bsky.app/starter-pack... Crystallography: bsky.app/starter-pack... Synchrotron&CryoEM: bsky.app/starter-pack...
I'm trying to find all the cool people sharing microscopy here. Help me 🤓🔬 go.bsky.app/Aaf8sKT
We're seeking feedback on our white paper on PeerReplication. Arthur, Kristen, Dyche, Anders, and I propose an alternative or augmentation to peer review, where key experiments are reproduced, adding robustness to published findings. zenodo.org/doi/10.5281/...
Great episode if you like thinking about sampling, basic stats, and paradoxes.
Allen Downey@allendowney.bsky.social · 3y agoThis week's guest on the SuperDataScience podcast is... me! We talked about Probably Overthinking It, the Overton Paradox, what it means to be normal, the expansion of the moral circle, and more. I hope you like it! www.superdatascience.com/podcast/make...
