Pablo Vergara

[Pablo Vergara @pabloivg]

Our Nature Communications paper is out!
We present CaliAli 🧠—a MATLAB toolbox for aligning & extracting neurons across 1p imaging sessions.
Tracks signals across months using vasculature-based alignment.

Open-source & documented.
Paper: https://t.co/bAHsGr0fJO

[Pablo Vergara @pabloivg]

Just updated CaliAli—a toolkit for longitudinal tracking in calcium imaging. It now auto-chunks each session; set your desired frames-per-batch and let it handle the rest. No manual file splitting, no RAM bottlenecks.

https://t.co/Mrz9uYkx8j

[Sakthivel Srinivasan @sakthivelsbio]

🚨 Our Nature Communications paper is out! We show that fear memory formation is supported by reactivating just a few adult-born neurons during REM sleep. 🧠💭
📖 [https://t.co/oyGEidSM0q]
#Neuroscience #Sleep #Memory

[Pablo Vergara @pabloivg]

Just updated CaliAli — a tool for tracking neurons in 1p calcium imaging across sessions

💾 Now with low-memory mode: split large sessions to process data even when single files don’t fit in RAM
https://t.co/Mrz9uYjZiL

Having trouble? Feel free to reach out — I reply weekly.

[David R. Liu @davidrliu]

Today in @ScienceMagazine we report the development of a laboratory-evolved CRISPR-associated transposase (evoCAST) that supports therapeutically relevant levels of RNA-programmable gene insertion in human cells, a collaboration with @SternbergLab.
1/13
https://t.co/ZLHtZm5Gmw

[日本経済新聞 電子版（日経電子版） @nikkei]

自転車「ながらスマホ」反則金1万2000円　26年4月から導入
https://t.co/Gq9bemEB0F

[Pablo Vergara @pabloivg]

Kudos to my former PI @masanorisaka !

[Pablo Vergara @pabloivg]

Our Nature Communications paper is out!
We present CaliAli 🧠—a MATLAB toolbox for aligning & extracting neurons across 1p imaging sessions.
Tracks signals across months using vasculature-based alignment.

Open-source & documented.
Paper: https://t.co/bAHsGr0fJO

[David @dav1dcg]

Silent Synapses in the Adult Brain

"review current evidence for silent synapses in the adult brain and explore the potential roles of these highly plastic structures."

https://t.co/u4BIiQSo6w

[Sakaguchi-lab @masanorisaka]

Thrilled to visit Rene’s lab! We had insightful discussions with great minds. Pablo’s CaliAli 1-P calcium imaging analysis tool garnered significant attention. Wrapped up with a fantastic American dinner alongside Rene’s wonderful team @Rene_Hen @pabloivg

[Sakaguchi-lab @masanorisaka]

Pablo and I had a wonderful time discussing science with Denise and her team, followed by a tasty Mexican lunch. Excited for future collaborations! Big thanks to Paul for helping make this meeting happen!🌮🧠 @ko3600 @denisejcai @pabloivg @Franklandlab

[Pablo Vergara @pabloivg]

@sjo09 @NatureNeuro Very cool work! I will be doing a Journal club on this paper next week

[Sheena Josselyn @sjo09]

Check out our latest paper. Here we attempted to bridge levels of analysis in memory research, linking receptors, dendritic spines, higher-order neuronal dynamics and behavior in mice. @NatureNeuro

https://t.co/Gnq2AeVy95
1/

[Bo Wang @BoWang87]

(1/5) Attention, Cellular Imaging Enthusiasts!

Thrilled to share that our Analysis "The Multi-modality Cell Segmentation Challenge: Towards Universal Solutions" has been published in Nature Methods (@NatureMethods) 🎉🎉🎉

Cell segmentation is a critical component of microscopy image analysis, but existing algorithms are often specialized for particular types of images or demand users to manually set hyper-parameters, posing challenges for biologists without a strong computational background.

To address these issues, we organized an international challenge at NeurIPS 2022 to promote the development of novel cell segmentation methods that excel across a wide array of microscopy images, imaging platforms, and tissue types.

🌐 Homepage: https://t.co/jJRujwDDwl
📄 Paper: https://t.co/FgfqoSLI05
🔬Data: https://t.co/P8i77CF62b
🏅Competition website: https://t.co/PA0LrBH7sd
👇 👇👇👇

[Avi Adhikari @Avi_UCLA]

Check out our new paper on feeding in Nature Communications 🔥! Along the way we answer a question that has puzzled philosophers for centuries: Does activation of periaqueductal gray (PAG) vgat cells make mice follow ping-pong balls? https://t.co/CFdM6I7f6N

[Denis Burdakov @DeBurdakov]

The eyes are windows to…the hypothalamus. Final cut now featuring locus coeruleus https://t.co/YtlvQnmE1p

[Pablo Vergara @pabloivg]

@ks_prokofeva @SfNJournals Good job Ksenia!! Very beautiful work!

[Kseniia Prokofeva @ks_prokofeva]

My first ever first author paper and PhD work is out in @SfNJournals ’ #JNeurosci!
In this paper, we’ve discovered a new neuronal circuit governing sleep/wake behavior. 1/10
https://t.co/eBgkeS3Rr0

[Pablo Vergara @pabloivg]

@LiorKir I don't see why it wouldn't work with 2p data. I am planning to include some experiment with 2p data ;). Thank you for the feedbac

[Pablo Vergara @pabloivg]

🧪🧠 Our latest #neuroscience paper presents #CaliAli, a game-changing neuron-tracking tool for one-photon calcium imaging! CaliAli excels at detecting weak signals & maximizes the number of trackable neurons. 🚀💡 @masanorisaka. 1/4
https://t.co/jXh4b8OIYP

[Luiz Pessoa @PessoaBrain]

𝗜𝗳 𝘁𝗵𝗲 𝗯𝗿𝗮𝗶𝗻 𝗶𝘀 𝗮 𝗰𝗼𝗺𝗽𝗹𝗲𝘅 𝘀𝘆𝘀𝘁𝗲𝗺 𝗮𝗿𝗲 𝗼𝗽𝘁𝗼𝗴𝗲𝗻𝗲𝘁𝗶𝗰 𝗺𝗮𝗻𝗶𝗽𝘂𝗹𝗮𝘁𝗶𝗼𝗻𝘀 𝗰𝗮𝘂𝘀𝗮𝗹?
https://t.co/hteImqFK72

[Pablo Vergara @pabloivg]

CaliAli shines in complex scenarios & outperforms other methods in precision, sensitivity, & stability. Whether studying representational drift, remote memory, neuron development, or multi-trial behavior, CaliAli is the tool to go! 🌟

Find #matlab code: https://t.co/k9h8UVcX5b

[Pablo Vergara @pabloivg]

Using a modified #miniscope with flexible light inputs @sakthivelsbio, we've paired optogenetics with calcium imaging to accurately identify tracked neurons.