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🚀 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...

17,655 views • 1 year ago •via X (Twitter)

23 Comments

Loïc A. Royer 💻🔬⚗️'s profile picture
Loïc A. Royer 💻🔬⚗️1 year ago

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.

Loïc A. Royer 💻🔬⚗️'s profile picture
Loïc A. Royer 💻🔬⚗️1 year ago

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:

Loïc A. Royer 💻🔬⚗️'s profile picture
Loïc A. Royer 💻🔬⚗️1 year ago

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

Loïc A. Royer 💻🔬⚗️'s profile picture
Loïc A. Royer 💻🔬⚗️1 year ago

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.

Loïc A. Royer 💻🔬⚗️'s profile picture
Loïc A. Royer 💻🔬⚗️1 year ago

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

Loïc A. Royer 💻🔬⚗️'s profile picture
Loïc A. Royer 💻🔬⚗️1 year ago

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!

Loïc A. Royer 💻🔬⚗️'s profile picture
Loïc A. Royer 💻🔬⚗️1 year ago

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

Loïc A. Royer 💻🔬⚗️'s profile picture
Loïc A. Royer 💻🔬⚗️1 year ago

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]

Loïc A. Royer 💻🔬⚗️'s profile picture
Loïc A. Royer 💻🔬⚗️1 year ago

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

Loïc A. Royer 💻🔬⚗️'s profile picture
Loïc A. Royer 💻🔬⚗️1 year ago

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

Loïc A. Royer 💻🔬⚗️'s profile picture
Loïc A. Royer 💻🔬⚗️1 year ago

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.

Loïc A. Royer 💻🔬⚗️'s profile picture
Loïc A. Royer 💻🔬⚗️1 year ago

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

Loïc A. Royer 💻🔬⚗️'s profile picture
Loïc A. Royer 💻🔬⚗️1 year ago

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

Loïc A. Royer 💻🔬⚗️'s profile picture
Loïc A. Royer 💻🔬⚗️1 year ago

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

Loïc A. Royer 💻🔬⚗️'s profile picture
Loïc A. Royer 💻🔬⚗️1 year ago

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.

Loïc A. Royer 💻🔬⚗️'s profile picture
Loïc A. Royer 💻🔬⚗️1 year ago

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.

Loïc A. Royer 💻🔬⚗️'s profile picture
Loïc A. Royer 💻🔬⚗️1 year ago

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.

Loïc A. Royer 💻🔬⚗️'s profile picture
Loïc A. Royer 💻🔬⚗️1 year ago

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! 👩‍🔬

Loïc A. Royer 💻🔬⚗️'s profile picture
Loïc A. Royer 💻🔬⚗️1 year ago

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.

Loïc A. Royer 💻🔬⚗️'s profile picture
Loïc A. Royer 💻🔬⚗️1 year ago

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

Loïc A. Royer 💻🔬⚗️'s profile picture
Loïc A. Royer 💻🔬⚗️1 year ago

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

Loïc A. Royer 💻🔬⚗️'s profile picture
Loïc A. Royer 💻🔬⚗️1 year ago

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

Loïc A. Royer 💻🔬⚗️'s profile picture
Loïc A. Royer 💻🔬⚗️1 year ago

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!

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