Saber C. Saharkhiz🔬📊💻🧬
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sabersaharkhiz.bsky.social
Saber C. Saharkhiz🔬📊💻🧬
@sabersaharkhiz.bsky.social
180 followers 480 following 39 posts
PhD-ing Neuroscience🧠 @uOttawaMed @OHRI
Mol Cell Dev Biologist using #AI4Microscopy to study Neurodevelopmental disorders.
Views are my own.
Posts Replies Media Videos
Reposted by Saber C. Saharkhiz🔬📊💻🧬
cellsdev.bsky.social
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...
Fig. 1. Comparative stages of transition from primary-to-posterior dorsal axial tissue formation. A dorsal and sagittal comparison of simplified CNS morphology in at the stage(s) of PNP closure (presumed junctional neurulation) between model organisms commonly used to study neurulation processes. A dorsal view of the shared structural characteristics between vertebrates at the posterior end depicts the anterior portion of the posterior processes which have completed neural tube closure and are in the process of segmenting somites from pre-formed PSM. Dashes mark the regions where primary and secondary neurulation processes occur at the same time and are overlapping (transition zone). Posterior to established neural tube and PSM is the region containing the NMP cell population, which are proliferating and maturing to form PSM and neural tube structures in an anterior to posterior direction. Mammals have formed roughly between 28 and 30 somites at neuropore closure (E9.5–10 in mouse, day 27 in humans). Avian have formed 22 somites at HH13, whereas amphibians have formed only 6–7 somites by NF 20. Finally, zebrafish have 21 somites at 19.5 hpf, which corresponds to the stage of neural primordium elongation, without convergence. Fig. 2. Antero-posterior progression of neurulation and somitogenesis. A graphical representation of primary and posterior processes that generate identical, uninterrupted structures through a transition zone. All vertebrates begin primary processes with a predetermined superficial neural cell layer, that converges at the midline to form a single lumen and pre-somitic mesoderm that condenses and segregates into somites. Posterior processes are established from a multi-potent NMP cell population that diverge to form separate neural and mesodermal populations and eventually forms structures indistinguishable from primary structures. These processes are hypothesized to occur at the same time within the transition zone, where primary processes progressively transition into posterior processes. Fig. 3. A comparison of naïve/pluripotent/stem cell populations and organizer regions. An organizer is capable of modulating the cell identities of neighboring cell populations through expression of various BMP antagonists and additional growth factors. Naïve cells are undifferentiated cells that are capable of developing into various cell types, dependent on the externally applied conditions. The diagrams are representative of the transplantation experiments completed by Spemann and Mangold, which illustrates the organizer's ability to induce neural identity from host cells.
December 12, 2025 at 2:00 PM
Reposted by Saber C. Saharkhiz🔬📊💻🧬
haoyin.bsky.social
CellSAM
A foundation model for Cell Segmentation
Segment Anything Model - Vision Transformer
cellsam.deepcell.org

Outperforming CellPose
Similar to Human

Single-cell spatial transcriptomics
Live-cell tracking
3D cell segmentation

@natmethods.nature.com 2025
www.nature.com/articles/s41...
December 11, 2025 at 12:36 PM
Reposted by Saber C. Saharkhiz🔬📊💻🧬
labwaggoner.bsky.social
Review @cp-cellchembiol.bsky.social @sbaratchi.bsky.social
Immunity in motion: The role of mechanics in macrophage biology
www.cell.com/cell-chemica...
December 9, 2025 at 3:59 PM
Reposted by Saber C. Saharkhiz🔬📊💻🧬
haoyin.bsky.social
Contribution of Gli1+ #AdventitialStemCell to #SmoothMuscleCell
❌Atherosclerosis
❌Wire-Injured Femoral Artery
✅Femoral Artery Anastomosis

1⃣Gli1-CreER;R26-tdT🐭
2⃣Myh11-Dre;Gli1-CreER;R26-IR1🐭
Gli1+ lineage➡️ZsG
Preexisting SMC➡️tdT

Adv Sci 2025
advanced.onlinelibrary.wiley.com/doi/10.1002/...
December 8, 2025 at 12:49 PM
Reposted by Saber C. Saharkhiz🔬📊💻🧬
isdb.bsky.social
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...
December 8, 2025 at 9:31 PM
Reposted by Saber C. Saharkhiz🔬📊💻🧬
bethcimini.bsky.social
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!
December 8, 2025 at 6:55 PM
Reposted by Saber C. Saharkhiz🔬📊💻🧬
jcellsci.bsky.social
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/...
Figure showing the interactive segmentation refinement in Toggle-Untoggle – de-selection, merging and manual annotation.
December 2, 2025 at 10:01 AM
sabersaharkhiz.bsky.social
One of the worst parts of training a Transformer-based model is spending hours stuck in the queue for a remote server!!!
December 4, 2025 at 5:19 AM
Reposted by Saber C. Saharkhiz🔬📊💻🧬
nature.com
Nature research paper: Inhibitory PD-1 axis maintains high-avidity stem-like CD8+ T cells

go.nature.com/48tM9dM
Inhibitory PD-1 axis maintains high-avidity stem-like CD8+ T cells - Nature
PD-1 blockade interferes with the selective expansion and maintenance of high-affinity TCR stem-like clones that have a critical role in effective checkpoint blockade therapy.
go.nature.com
December 1, 2025 at 9:18 AM
Reposted by Saber C. Saharkhiz🔬📊💻🧬
rachaelott.bsky.social
Here’s a side-by-side comparison of the reference image input (from Sachs et al., 2009) and the AI generated figure (below)
November 24, 2025 at 7:49 PM
Reposted by Saber C. Saharkhiz🔬📊💻🧬
rachaelott.bsky.social
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
This is a 100% AI generated figure created using Gemini 3 (Nano Banana Pro) on Adobe Firefly.
November 24, 2025 at 7:11 PM
sabersaharkhiz.bsky.social
WHat? ARe YoU SEriOus? Bullshit?????? @natureportfolio.nature.com
November 22, 2025 at 5:42 PM
Reposted by Saber C. Saharkhiz🔬📊💻🧬
daniellebeckman.bsky.social
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
Fluorescence confocal microsocopy image of the hippocampus
November 14, 2025 at 6:37 PM
sabersaharkhiz.bsky.social
And many research papers confirm that quote as well!
November 14, 2025 at 2:30 AM
sabersaharkhiz.bsky.social
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.
November 14, 2025 at 1:58 AM
sabersaharkhiz.bsky.social
OHRI Poster presentation
November 13, 2025 at 11:46 PM
Reposted by Saber C. Saharkhiz🔬📊💻🧬
frezzalab.bsky.social
A whole-brain single-cell atlas of circadian neural activity in mice | Science www.science.org/doi/10.1126/...
A whole-brain single-cell atlas of circadian neural activity in mice
The mammalian brain comprises numerous anatomical regions with distinct functions despite their extensive connectivity. However, how spontaneous neural activity is coordinated across regions over the ...
www.science.org
November 13, 2025 at 7:07 PM
sabersaharkhiz.bsky.social
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
November 9, 2025 at 5:39 AM
Reposted by Saber C. Saharkhiz🔬📊💻🧬
mag2art.bsky.social
Beating iPSC-derived heart muscle cells videoed through a microscope. Alpha-actinin-2 is shown. #CellBiology
November 9, 2025 at 3:12 AM
Reposted by Saber C. Saharkhiz🔬📊💻🧬
drannecarpenter.bsky.social
Required reading for cell biologists to get a sense of basic statistical principles!

www.nature.com/articles/s41...
Ten essential tips for robust statistics in cell biology - Nature Cell Biology
Statistical thinking is a core part of solid, trustworthy biology. However, many studies still include insufficient sample sizes, have poor experimental design or select an incorrect statistical metho...
www.nature.com
November 4, 2025 at 7:23 PM
Reposted by Saber C. Saharkhiz🔬📊💻🧬
labogden.bsky.social
It's Halloween 🎃 #FlourescenceFriday! Here is a microscopic pumpkin generated by showing a cell nucleus in 🟠 with the primary cilium "stem" in 🟢! I hope everyone has a spooky 👻 day! 🔬 by @stjuderesearch.bsky.social grad student Christina Wang. 🧪
Confocal micrograph of a nucleus stained in orange and the primary cilium in green. The color combination makes it look like a pumpkin.
October 31, 2025 at 3:14 PM
Reposted by Saber C. Saharkhiz🔬📊💻🧬
haoyin.bsky.social
#Atherosclerosis Epitranscriptomics

Mettl3-YTHDF3⏫m6A-MTRFA mRNA in SMCs➡️
⏫cholesterol-induced Mφ-like phenotype

SMC Mettl3 KO🐭+HFD AAV-PCSK9➡️
⏬Lesion burden, necrotic core, Mφ
👉Abolishes SMC contribution to lesion!
👉Reverted by AAV9-SM22-MRTFA

#CardiovascRes 2025
academic.oup.com/cardiovascre...
October 30, 2025 at 8:23 PM
sabersaharkhiz.bsky.social
Happy Cyrus The Great Day! (October 29th)
Remembering #Cyrus_The_Great
📷 @ShahbanouFarah @PahlaviReza
October 29, 2025 at 7:07 PM
Reposted by Saber C. Saharkhiz🔬📊💻🧬
jcb.org
Mechanical coordination between anaphase A and B drives asymmetric chromosome segregation, say Ana Dias Maia Henriques, Julien Dumont, Gilliane Maton and colleagues @ijmonod.bsky.social: rupress.org/jcb/article/...

#Development #CellCycle #CellDivision #Celegans #Mitosis
October 29, 2025 at 1:31 PM
Reposted by Saber C. Saharkhiz🔬📊💻🧬
bethcimini.bsky.social
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 !
October 27, 2025 at 6:20 PM