Loïc A. Royer 💻🔬⚗️'s banner

Loïc A. Royer 💻🔬⚗️

@loicaroyer • 6,549 subscribers

Director @biohub SF #zfish #devbio #zebrahub #AI #Lightsheet #Imaging co-creator of @napari_imaging

Shorts

1/ How does one cell become an entire animal? We can now film it in 3D, but turning those movies into accurate cell tracks is brutally hard. Enter our new #Kaggle challenge: $60K prize pool, to help crack 3D+time cell tracking at scale! biohub

1/ How does one cell become an entire animal? We can now film it in 3D, but turning those movies into accurate cell tracks is brutally hard. Enter our new #Kaggle challenge: $60K prize pool, to help crack 3D+time cell tracking at scale! biohub

11,120 views

🔊 Exciting AI Research Opportunity! my team at Chan Zuckerberg Biohub Network SF is hiring a Research Scientist to develop foundational AI models for BioImage analysis. Join us to work on cutting-edge ML/CV! 💻🔬🧪🧠 #AIJobs #ML Think of it as a "postdoc on steroids" in AI/ML/CV. You will have access to world-class computing: one of the largest nonprofit #AI clusters (1000x H100)! , unique datasets, and an incredibly supportive collaborative environment!

🔊 Exciting AI Research Opportunity! my team at Chan Zuckerberg Biohub Network SF is hiring a Research Scientist to develop foundational AI models for BioImage analysis. Join us to work on cutting-edge ML/CV! 💻🔬🧪🧠 #AIJobs #ML Think of it as a "postdoc on steroids" in AI/ML/CV. You will have access to world-class computing: one of the largest nonprofit #AI clusters (1000x H100)! , unique datasets, and an incredibly supportive collaborative environment!

15,258 views

We seek a Bachelor- or Master-level Instrumentation Engineer. Enjoy writing well-architected instrument control software 💻? Like to tinker with electronics ⚡️and hardware 📠? Apply! The microscopes 🔬 that we design, build, and operate can produce these beautiful videos! Please retweet! 🙏

We seek a Bachelor- or Master-level Instrumentation Engineer. Enjoy writing well-architected instrument control software 💻? Like to tinker with electronics ⚡️and hardware 📠? Apply! The microscopes 🔬 that we design, build, and operate can produce these beautiful videos! Please retweet! 🙏

14,202 views

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🚨 #ChatGPT + napari 🚨 Releasing my latest weekend project: Omega, an autonomous LLM agent that writes image processing and analysis code, fixes its mistakes, accesses the napari viewer, makes widgets, & more! OpenAI #OmegaAgent

🚨 #ChatGPT + napari 🚨 Releasing my latest weekend project: Omega, an autonomous LLM agent that writes image processing and analysis code, fixes its mistakes, accesses the napari viewer, makes widgets, & more! OpenAI #OmegaAgent

Loïc A. Royer 💻🔬⚗️

328,878 views • 3 years ago

🚨Big news! Five years in the making, our Zebrahub paper is now published in #Cell 🎉. We’ve built a timecourse atlas of zebrafish embryonic development, combining #scRNAseq data and #lightsheet live imaging, and delved deep into the dynamics of key progenitors. Explore the datasets here: Led by Merlin Lange with key contributions by Alejandro Granados, Shruthi VijayKumar, Jordão Bragantini, Sarah Ancheta and YangJoon Kim #zebrahub #devbio #cell #Biology #imaging Cell @czbbiohub #CZBiohubS

🚨Big news! Five years in the making, our Zebrahub paper is now published in #Cell 🎉. We’ve built a timecourse atlas of zebrafish embryonic development, combining #scRNAseq data and #lightsheet live imaging, and delved deep into the dynamics of key progenitors. Explore the datasets here: Led by Merlin Lange with key contributions by Alejandro Granados, Shruthi VijayKumar, Jordão Bragantini, Sarah Ancheta and YangJoon Kim #zebrahub #devbio #cell #Biology #imaging Cell @czbbiohub #CZBiohubS

Loïc A. Royer 💻🔬⚗️

83,737 views • 1 year ago

We present #Zebrahub: a timecourse atlas of zebrafish embryonic development, combining #scRNAseq time-course data with #lightsheet live imaging. Explore our seq. and imaging datasets interactively at 1/n

We present #Zebrahub: a timecourse atlas of zebrafish embryonic development, combining #scRNAseq time-course data with #lightsheet live imaging. Explore our seq. and imaging datasets interactively at 1/n

Loïc A. Royer 💻🔬⚗️

86,027 views • 3 years ago

Super stoked that Jordão Bragantini 's napari plugin for Meta's Segment Anything Model 2: napari-sam2, as well as our cell tracking software ultrack were showcased during Chris Cox's Keynote at Meta's Connect 2024. Jordao and I were in the audience; it was great fun! Chan Zuckerberg Biohub Network

Super stoked that Jordão Bragantini 's napari plugin for Meta's Segment Anything Model 2: napari-sam2, as well as our cell tracking software ultrack were showcased during Chris Cox's Keynote at Meta's Connect 2024. Jordao and I were in the audience; it was great fun! Chan Zuckerberg Biohub Network

Loïc A. Royer 💻🔬⚗️

41,061 views • 1 year ago

📡🧵 Excited to release two #bioRxiv preprints! The first preprint is: "Zebrahub-Multiome: Uncovering Gene Regulatory Network Dynamics During Zebrafish Embryogenesis" We present a comprehensive time-resolved single-cell multiomic atlas of zebrafish development. Integrating scATAC-seq and scRNA-seq from 94,000+ cells, we map gene regulatory networks across six key stages of embryogenesis (10 to 24 hpf). A major accomplishment by YangJoon Kim co-led by Merlin Lange with experiments by Shruthi VijayKumar #Zebrahub-Multiome is a sequel to our transcriptomic and imaging atlas of zebrafish development. #zebrafish #development #ATACseq #cell #biology #sequencing Chan Zuckerberg Biohub Network #CZBiohubSF Biohub Note: We sent two preprints simultaneously yesterday, and this is the first one to come out... I will append to this thread when the second one is out...

📡🧵 Excited to release two #bioRxiv preprints! The first preprint is: "Zebrahub-Multiome: Uncovering Gene Regulatory Network Dynamics During Zebrafish Embryogenesis" We present a comprehensive time-resolved single-cell multiomic atlas of zebrafish development. Integrating scATAC-seq and scRNA-seq from 94,000+ cells, we map gene regulatory networks across six key stages of embryogenesis (10 to 24 hpf). A major accomplishment by YangJoon Kim co-led by Merlin Lange with experiments by Shruthi VijayKumar #Zebrahub-Multiome is a sequel to our transcriptomic and imaging atlas of zebrafish development. #zebrafish #development #ATACseq #cell #biology #sequencing Chan Zuckerberg Biohub Network #CZBiohubSF Biohub Note: We sent two preprints simultaneously yesterday, and this is the first one to come out... I will append to this thread when the second one is out...

Loïc A. Royer 💻🔬⚗️

39,773 views • 1 year ago

📡🧵 Excited to release our preprint: Ultrack: Pushing the Limits of Cell Tracking Across Biological Scales A tour-de-force by Jordão Bragantini, #Ultrack is a versatile, highly accurate, and fast ILP-based cell tracking software for 2D, 3D, and multicolor datasets. It has convenient napari and Fiji plugin interfaces and built-in HPC cluster support. #cell_tracking #microscopy #devbio Chan Zuckerberg Biohub Network

📡🧵 Excited to release our preprint: Ultrack: Pushing the Limits of Cell Tracking Across Biological Scales A tour-de-force by Jordão Bragantini, #Ultrack is a versatile, highly accurate, and fast ILP-based cell tracking software for 2D, 3D, and multicolor datasets. It has convenient napari and Fiji plugin interfaces and built-in HPC cluster support. #cell_tracking #microscopy #devbio Chan Zuckerberg Biohub Network

Loïc A. Royer 💻🔬⚗️

33,564 views • 1 year ago

🧬🔬🧪 🎉 Our team at Chan Zuckerberg Biohub Network is thrilled to share TWO companion papers out today in @NatureMethods! 📦 Ultrack — robust, scalable nD cell tracking 🌐 inTRACKtive — a beautiful, open-source web viewer for lineage exploration Let’s dive in! 👇 (LINKS BELOW)

🧬🔬🧪 🎉 Our team at Chan Zuckerberg Biohub Network is thrilled to share TWO companion papers out today in @NatureMethods! 📦 Ultrack — robust, scalable nD cell tracking 🌐 inTRACKtive — a beautiful, open-source web viewer for lineage exploration Let’s dive in! 👇 (LINKS BELOW)

Loïc A. Royer 💻🔬⚗️

18,390 views • 11 months ago

🚀 Thrilled to announce #inTRACKtive: a web-based tool for exploring massive cell-tracking datasets, no software installation required! Just open your browser and dive into terabytes of developmental biology data. We used it to build the virtual of tracked embryonic development datasets 🐭🪰🪱🪲🐠, but you can also use it for your own data! 🔬 Preprint: Repository: This project was spear-headed by Teun Huijben, together with engineers Andrew Sweet and @aganders3 from Biohub @czbbiohub #CZBiohubSF #devbio #tracking #web #visualization 🧵1/n

🚀 Thrilled to announce #inTRACKtive: a web-based tool for exploring massive cell-tracking datasets, no software installation required! Just open your browser and dive into terabytes of developmental biology data. We used it to build the virtual of tracked embryonic development datasets 🐭🪰🪱🪲🐠, but you can also use it for your own data! 🔬 Preprint: Repository: This project was spear-headed by Teun Huijben, together with engineers Andrew Sweet and @aganders3 from Biohub @czbbiohub #CZBiohubSF #devbio #tracking #web #visualization 🧵1/n

Loïc A. Royer 💻🔬⚗️

17,680 views • 1 year ago

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