Saber C. Saharkhiz🔬📊💻🧬
DVM; PhD-ing Neuroscience🧠 @uOttawaMed @OHRI
Molecular, Cell & Developmental Biologist using #AI4Microscopy to study Neurodevelopmental disorders.
Views are my own.
- Reposted by Saber C. Saharkhiz🔬📊💻🧬Our #preprint list is up on FocalPlane. This list focusses on the latest tools in bioimage analysis. Let us know if you have any recommendations to add to our list. focalplane.biologists.com/2026/02/06/m...
- Reposted by Saber C. Saharkhiz🔬📊💻🧬Ep 24 - Understanding your thresholding options is the diff between a win and a loss in SO MANY workflows - gain that intuition, and SO MUCH is easier. The 1st of 3 episodes discussing why - inspired by OUR FIRST REAL READER QUESTION. @erinweisbart.bsky.social and I are actual advice columnists now!
- Ep 23 - So what actually IS CellPainting anyway? You may have heard of it if you're say, a fan of the @drannecarpenter.bsky.social - @shantanu-singh.cc lab (and who isn't????), but what, you know, is it? Let @erinweisbart.bsky.social break it down for you! youtu.be/9-d6DoHtgUY
- 📷 iPhone 17 Pro Max 📍Ottawa
- Reposted by Saber C. Saharkhiz🔬📊💻🧬Ep 23 - So what actually IS CellPainting anyway? You may have heard of it if you're say, a fan of the @drannecarpenter.bsky.social - @shantanu-singh.cc lab (and who isn't????), but what, you know, is it? Let @erinweisbart.bsky.social break it down for you! youtu.be/9-d6DoHtgUY
- Ep 22 - while we all love CellProfiler (right??), we know that often the challenging part is handling the "bookkeeping" to get your data into it in the first place. @erinweisbart.bsky.social and I do a quick overview, and then point to great longer-form materials. Welcome to AE/DB 2026!
- New year, new paper — and my first paper of the year! Happy to share our newly published open-access article in Stem Cell Reviews and Reports: link.springer.com/article/10.1... Many thanks to my collaborators in Poland and the US for their support. #StemCell #CellBiology
- Reposted by Saber C. Saharkhiz🔬📊💻🧬Ep 22 - while we all love CellProfiler (right??), we know that often the challenging part is handling the "bookkeeping" to get your data into it in the first place. @erinweisbart.bsky.social and I do a quick overview, and then point to great longer-form materials. Welcome to AE/DB 2026!
- Reposted by Saber C. Saharkhiz🔬📊💻🧬A thorough review of deep-learning approaches (I prefer that to "AI") for enhancing super-resolution microscopy by @orangeroad2017.bsky.social, Yang Zhang and colleagues in @natmethods.nature.com: doi.org/10.1038/s415...
- Reposted by Saber C. Saharkhiz🔬📊💻🧬It’s certainly been a year, but I’m incredibly grateful that earlier in 2025 I was promoted to Associate Professor with tenure! Huge thanks to you all for promoting our work here and on the other site, for talk invites, for writing letters of support, and to the lab for all their contributions. 🥂
- Reposted by Saber C. Saharkhiz🔬📊💻🧬Single-molecule live-cell fluorescence in situ hybridization uses an RNA-targeting CRISPR–Csm complex to image and track endogenous RNAs go.nature.com/3EJPKsM rdcu.be/eUK9K
- Just came across this book from a friend (Iman Khorsand)🤝🏼 A holiday must-read 🫶🏻👌🏻📚
- My talk at the #I2K 2025 conference is now available online. There are also many other great talks worth checking out. My full talk is on their YouTube and includes a hands-on walkthrough of how to use VNC-Dist: youtu.be/ZxngGrqAr_Y?...
- Excited to share the 1st part of my PhD work in @plosone.org ! 🚀 Progress in biology needs not only new ideas but also #workflow_automation Open Access: 📃paper: journals.plos.org/plosone/arti... 💻Code: github.com/C-elegans-VN... #CellBiology #Neuroscience #DeepLearning #Bioimage_Analysis
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- Reposted by Saber C. Saharkhiz🔬📊💻🧬A new paper out in @natmethods.nature.com introduces NimbusImage, a cloud-computing platform for image analysis ft. William Niu (SAS), Jingxin Li (@cambupenn.bsky.social), @aofarrell.bsky.social (Bioengineering) & @arjunraj.bsky.social (@penngenetics.bsky.social) www.nature.com/articles/s41...
- “Nobody's found anything in the universe that's non computable, so far!” —Demis Hassabis
- Reposted by Saber C. Saharkhiz🔬📊💻🧬If you use linkedin connect with @sabersaharkhiz.bsky.social he is posting some interesting material.
- If you’re interested in bioimage analysis tools, my LinkedIn post(s) are worth a read. #Bioimage_Analysis #Microscopy #CellBiology #AI4Microscopy
- Reposted by Saber C. Saharkhiz🔬📊💻🧬ICYMI, our #preprint list is now up on FocalPlane, highlighting the latest research using #microscopy to answer questions in #biology. As always, send us any recommendations for preprints that we've missed: focalplane.biologists.com/2025/12/12/m...
- If you’re interested in bioimage analysis tools, my LinkedIn post(s) are worth a read. #Bioimage_Analysis #Microscopy #CellBiology #AI4Microscopy
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- Reposted by Saber C. Saharkhiz🔬📊💻🧬Vertebrates can use entirely different mechanisms to generate its anterior and posterior dorsal tissue. In this thorough review from the lab of Lance Davidson, different morphogenetic events are compared between the front and the back in a developing embryo. Check it out: doi.org/10.1016/j.cd...
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- Reposted by Saber C. Saharkhiz🔬📊💻🧬Do your samples move out of view? Tired of manually adjusting the stage? Introducing DySTrack developed by @zimengwu33.bsky.social and Jonas Hartmann from UCL, a tool that can be integrated into modern microscopes to automate the tracking of moving samples. #MicroscopyMonday doi.org/10.64898/202...
- Reposted by Saber C. Saharkhiz🔬📊💻🧬20 eps - wow! Today, @erinweisbart.bsky.social and I introduce BioimagingGuide.org, a fantastic resource we made in partnership with @bioimagingna.bsky.social , your guide to "what you don't know you don't know" about imaging and analysis. Friendly and in 4 languages (and counting!); check it today!
- Reposted by Saber C. Saharkhiz🔬📊💻🧬In their Tools and Resources article, Nina Grishchenko, Michael Olson and colleagues present Toogle-Untoogle, a cell segmentation tool with an interactive user verification interface. journals.biologists.com/jcs/article/...
- One of the worst parts of training a Transformer-based model is spending hours stuck in the queue for a remote server!!!
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- Reposted by Saber C. Saharkhiz🔬📊💻🧬Here’s a side-by-side comparison of the reference image input (from Sachs et al., 2009) and the AI generated figure (below)
- Reposted by Saber C. Saharkhiz🔬📊💻🧬Gemini 3 created this figure in under 30 seconds from a couple reference images and a one sentence prompt So I’m at a loss for words, honestly #MicroscopyMonday
- WHat? ARe YoU SEriOus? Bullshit?????? @natureportfolio.nature.com
- Reposted by Saber C. Saharkhiz🔬📊💻🧬The Society for Neuroscience meeting starts tomorrow! I prepared some microscopy images for display at the convention center in San Diego. Let me know if you see one of my images around! 🤓 🔬 🧠 @sfn.org #SfN25 #FluorescenceFriday
- And many research papers confirm that quote as well!
- I always start my talks with this slide to encourage the audience, especially biologists 🧬🔬, to learn coding. This quote from the legendary Steve Jobs 🧑🏻💻 reshaped my research path almost 5 years ago, when I was a biologist with no computer science background.
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- Do you know how many genetic tools used to visualize only the nuclei of these neurons? (From my PhD work) 1. Endogenous CRISPR knock-in tag 2. Promotor transgene fused to Histone 3. Endogenous CRISPR knock-in dual color tag with self-cleaving peptide T2A fused to Histone. #FluorescenceFriday
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- Reposted by Saber C. Saharkhiz🔬📊💻🧬Required reading for cell biologists to get a sense of basic statistical principles! www.nature.com/articles/s41...
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- Happy Cyrus The Great Day! (October 29th) Remembering #Cyrus_The_Great 📷 @ShahbanouFarah @PahlaviReza
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- Reposted by Saber C. Saharkhiz🔬📊💻🧬Episode 17 - perhaps my favorite yet. How do you write a forum.image.sc post that will get you the answers you need without revealing information you don't want to tell? @erinweisbart.bsky.social and I go through what the experts need to know to help you. Post your sci q's today on forum.image.sc !
- Episode 16 - Learn more about the Cell Painting Gallery, a free repository of nearly a petabyte of images and imaging data, curated by the incredibly talented @erinweisbart.bsky.social . Truly a goldmine for big-data lovers everywhere!
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- Reposted by Saber C. Saharkhiz🔬📊💻🧬💡Just presented our new paper at the @iccv.bsky.social BioImage Computing workshop: cubic: CUDA-accelerated 3D Bioimage Computing. We introduce a simple way to add GPU acceleration to scikit-image–based bioimage processing pipelines by swapping import statements. 🧵 1/6 #iccv2025
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- Reposted by Saber C. Saharkhiz🔬📊💻🧬Today for #FluorescenceFriday I’m sharing a 👻Halloween-themed🎃 neural crest explant “web of cells” from Julia Godinez, a 4th year @ucdavis.bsky.social graduate student in the lab. She is studying mechanisms driving conserved and divergent cranial neural crest migration and differentiation. #DevBio
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- My son is so tired💤🤭😂🦜🪶
- Reposted by Saber C. Saharkhiz🔬📊💻🧬Episode 16 - Learn more about the Cell Painting Gallery, a free repository of nearly a petabyte of images and imaging data, curated by the incredibly talented @erinweisbart.bsky.social . Truly a goldmine for big-data lovers everywhere!
- Reposted by Saber C. Saharkhiz🔬📊💻🧬15 years in the making, we confirmed that mitochondria - the powerhouse of the cell - have an unusual localization in patients who experience psychosis (including schizophrenia and bipolar disorders). You’ll never guess what kind of patient cells we used to make this discovery… 🧵
- Reposted by Saber C. Saharkhiz🔬📊💻🧬Segment large images without tiling artifacts: sharing our work that should have been presented at ICCV in 2 weeks - the brilliant first author Elena can’t go because of visa issues. The paper: arxiv.org/abs/2503.19545 1/🧵
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- Just reached a small but meaningful milestone, 100+ citations in under 3 years since starting grad school. Grateful that my workare being recognized, and reminded of why I began this journey back at #Université_de_Sherbrooke and continued at the #University_of_Ottawa !
- Reposted by Saber C. Saharkhiz🔬📊💻🧬My entry for today’s #FluorescenceFriday: a pupal #Drosophila testis with muscles expressing 🔵 lifeact & 🔴 RFP-nls Honored & grateful to receive an honorable mention at @healthcare.nikon.com Nikon Small World 🌍🔬✨ 🔗 www.nikonsmallworld.com/galleries/20... #NikonSmallWorld #Microscopy #ScienceArt
- Reposted by Saber C. Saharkhiz🔬📊💻🧬💫NEW: @telemanlab.bsky.social & co demonstrate that #AMPK can be activated by signaling metabolite, #adenosine, under non-stress conditions during #Drosophila development. The intestine regulates adenosine levels, thus, remotely controlling wing disc AMPK activation and growth. bit.ly/4gX6njF
- Reposted by Saber C. Saharkhiz🔬📊💻🧬#fluorescencefriday special. Half marmoset 🧠 cleared and stained using SHIELD and imaged by lightsheet microscopy. Courtesy of Jesleen Saini @shahrzadbahrampour.bsky.social and @stefan-everling.bsky.social
- Reposted by Saber C. Saharkhiz🔬📊💻🧬Sharing this excellent review now out from postdoc Sarah McLarnon! Lots of useful info on 3D imaging, quantification of imaging data, and how this has been applied to the kidney. And since it's #FluorescenceFriday, sharing a figure with our own imaging data! www.sciencedirect.com/science/arti...
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- Since my work combines #biology and #computer_science, I was surprised to learn that in computer science, top research is usually published in prestigious conferences (like NeurIPS or MICCAI), which carry the same weight as journals such as Nature in other fields!
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- Reposted by Saber C. Saharkhiz🔬📊💻🧬Halfway to I2K is BACK, friends of all kinds! Last year, 650 people attended 30+ TOTALLY FREE image analysis workshops of all kinds, across many timezones. If you make image analysis software and want to teach it, workshop submissions are open now! We'd love to have your tool highlighted.
- #HappyFluorescenceFriday! #microscopycommunity- want to learn open source image analysis or share your knowledge to help others? We’ve got a FREE virtual workshop Nov 17-19! Now accepting workshop session applications! Learn more & sign up: buff.ly/esGIotD
