📡🧵 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...show more

2/ 🐠 Zebrahub-Multiome offers interactive data exploration via CZ #CellxGene and interactive figures powered by #Streamlit. Dive into the time-resolved and cell-type-specific complexities of chromatin accessibility and gene regulatory networks during zebrafish embryogenesis with unprecedented detail! #zebrahub #grn #devbio

3/ 📊 Check out the #CellxGene interactive visualisations! You can explore all the data, just #RNA-seq, just #ATAC-seq, or the joint RNA-seq + ATAC-seq! and even perform differential gene expression analysis directly in the browser!

4/ 🧬 Our interactive figures mirror most panels in our manuscript. You can explore #chromatin co-accessibility and gene track plots for all zebrafish genes. We display distal and proximal regulatory elements (peaks) along with protein-coding regions for each gene. Peaks are highly correlated with transcription start sites, computed using cicero. Links to #ZFIN and #Ensembl provide additional context. Moreover, for each time point, we present time-resolved scatter plots comparing gene activity (#ATAC) and gene expression (RNA). Each point represents a metacell, computed using #SEACell, colored by the most prevalent cell type.

5/ 🧪 We computed gene regulatory networks (#GRNs) between transcription factors and genes for all cell types and developmental stages. You can explore this data per developmental stage in our interactive figure:

6/ 🧪 Or explore the same #GRNs but by cell type!

7/ 🗺️ We dived deeper and looked at mesodermal and neuro-ectodermal lineages using a metacell approach to denoise the data. We could compute wild-type metacell-metacell transition probabilities and look at the effect of transcription factor virtual knockouts in a temporally resolved manner. You can do virtual knockouts experiments for any relevant TF in the browser! This is great for generating hypotheses that would need to be validated experimentally... We are working on generalizing this to all cell types.

8/ 🔍 Zebrahub-multiome resource offers insights into zebrafish development, from gene regulation to cell fate decisions. Perfect for developmental biologists, geneticists, and computational biologists!

9/ 🤝 This work would not have been possible without the great work and help of the whole team: @yangjoonkim, @Shruthi94Vijay, Benjamin Iovino, @ale_agranados, @Sarah_E_Ancheta, @hoover_zhao, @kyleawayan, Amanda Seng, @mikeborjatweets, Sheryl Paul, Honey Mekonen, Ritwicq Arjyal, Angela Detweiler, Norma Neff, @Merlin_Lange, collaborators, all San Francisco biohubbers!

10/ We are deeply grateful to CZB SF donors Priscilla Chan and Mark Zuckerberg for their generous support, which made this research possible.

11/ We expect and hope for a robust and enthusiastic discussion with the community and welcome feedback, ideas, and suggestions! Reach out at [email protected], [email protected] and [email protected]

12/ 🐠 Dive into the depths of zebrafish development with Zebrahub-Multiome! #DevelopmentalBiology #SingleCell #Multiomics #Zebrafish

⚡️The second preprint just came out on #bioRxiv! ⚡️

🚀 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 @TeunHuijben, together with engineers Andrew Sweet and @aganders3 from @cziscience @czbbiohub #CZBiohubSF #devbio #tracking #web #visualization 🧵1/n

2/ 💻 The size and complexity of microscopy datasets, spanning terabytes and thousands of cells, require expertise and resources, which limits accessibility. We present #inTRACKtive: a user-friendly web-based client-side solution for visualizing and interacting with large cell tracking datasets.

3/ 🌟 Why is #inTRACKtive a game changer? It enables researchers to visualize, analyze, and share cell-tracking datasets – all in real-time, in your browser, without downloading a single file. You can select specific cells or groups of cells and trace their lineages interactively through time, perfect for virtual fate-mapping experiments! 💻📊 #CellTracking

4/ 🐠 #inTRACKtive can handle enormous cell tracking datasets, like the zebrafish datasets from with 10-thousands of cells over hundreds of frames.

5/ 🐣 With this technology at hand, we could not resist the temptation to build the Virtual Embryo Zoo ( a showcase of cell-tracking datasets from 6 model organisms, including zebrafish, Drosophila, and mouse. We sourced the best tracking datasets from the community! Explore them interactively, trace lineages, and download tracking data for further analysis! 🐟🐭 #Embryogenesis

6/ 🏆 Within the Virtual Embryo Zoo, users can visualize the tracked datasets with #inTRACKtive, download the complete tracking data (ready to visualize in @napari_imaging ) and see details of the datasets.

7/ 🤖 The #inTRACKtive platform is optimized for interaction with large-scale datasets. The key innovation is using a specialized cell tracking format based on #Zarr, which enables asynchronous, lazy data loading. We provide scripts to convert tracking data into the required Zarr format.

8/ 📱 #inTRACKtive works in any browser, including on tablets and smartphones, offering flexibility in how users interact with the data. To utilize the full UI functionalities, a larger screen and keyboard are recommended.

9/ 🔗 With #inTRACKtive, your exact viewing configuration - cells, zoom level, selections, and more — can be shared via a simple hyperlink. Collaboration has never been easier! 👩‍🔬

10/ 🛜 The #inTRACKtive platform is open source ( and has multiple use cases: (i) to explore the Virtual Embryo Zoo, (ii) to visualize your own cell tracking data, and (iii) to host your own customizable instance of the viewer.

11/ 🙌 All credits to the amazing team that made #inTRACKtive and the virtual embryo zoo happen: @TeunHuijben, @aganders3, Andrew Sweet, @ErinHoops, Connor Larsen, @kyleawayan, @jobragantini, and Chi-Li Chiu

12/ 🙌 A huge thank you to the incredible labs and researchers who made their data publicly available or kindly shared it with us upon request to the Virtual Embryo Zoo ( #OpenScience Hari Shroff, Mark Moyle, @GuignardLab, @PatrickLemaire_, Grégoire Malandain, @Merlin_Lange, @czbiohub, @PavelTomancak, @Jain_Akanksha_, Philipp Keller, Fernando Amat, Kate McDole, @haesleinhuepf

13/ 🙏We are deeply grateful to CZB SF donors Priscilla Chan and Mark Zuckerberg for their generous support, which made this research possible.

14/ ☎️ If you want to contribute to this project, have a cool dataset that we can feature in the Virtual Embryo Zoo, or need help with cell tracking (with #ultrack), feel free to reach out!