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#MicroscopyMonday 🔬 — A 3D reconstruction of a cleared mouse embryo labeled for neurons (magenta) and muscles (cyan). This type of imaging lets researchers can image deep into biological tissue to study neuronal morphology in an intact animal or embryo. Credit: G Carrillo

Marine Biological Laboratory (MBL)

26,142 subscribers

21,069 просмотров • 1 год назад •via X (Twitter)

Образование Наука и технологии #MicroscopyMonday

Anya Rossi• Live Now

Private livecam show

Комментарии: 4

Фото профиля no time for space

no time for space1 год назад

amazing !

Фото профиля Sedge💧🦠🔬 😷💉

Sedge💧🦠🔬 😷💉1 год назад

Light-sheet microscopy?

Фото профиля Marine Biological Laboratory (MBL)

Marine Biological Laboratory (MBL)1 год назад

A stage-scanning line confocal developed at the MBL!

Фото профиля The Prince Lab

The Prince Lab1 год назад

@ArthropodLegs What was the clearing protocol?

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We’re hiring at Deep Piction 🧠🔬 We are looking for a Scientist – Tissue Clearing & Image Analysis (m/f/d) to join our team in Munich. You will help drive tissue-clearing, light-sheet microscopy, and quantitative 3D imaging projects across internal R&D programs and collaborations with biotechnology and pharmaceutical partners. The role combines hands-on experimental work, project ownership, workflow development, and close collaboration with our AI and image-analysis teams. We’re looking for someone with strong experience in tissue clearing, fluorescence microscopy, light-sheet imaging, and large-scale 3D image analysis. Please apply with one single PDF containing your CV and cover letter to: hr@deeppiction.com Subject: Scientist – Tissue Clearing & Image Analysis (DP-TC-2026-01) Applications will be reviewed on a rolling basis until the position is filled.

We’re hiring at Deep Piction 🧠🔬 We are looking for a Scientist – Tissue Clearing & Image Analysis (m/f/d) to join our team in Munich. You will help drive tissue-clearing, light-sheet microscopy, and quantitative 3D imaging projects across internal R&D programs and collaborations with biotechnology and pharmaceutical partners. The role combines hands-on experimental work, project ownership, workflow development, and close collaboration with our AI and image-analysis teams. We’re looking for someone with strong experience in tissue clearing, fluorescence microscopy, light-sheet imaging, and large-scale 3D image analysis. Please apply with one single PDF containing your CV and cover letter to: [email protected] Subject: Scientist – Tissue Clearing & Image Analysis (DP-TC-2026-01) Applications will be reviewed on a rolling basis until the position is filled.

Ali Max Erturk

10,921 просмотров • 1 месяц назад

We are thrilled to share that our first paper from my new lab, Spateo ( for spatiotemporal modeling of molecular holograms, is now online in Cell: Spateo is a comprehensive analytical framework for 3D whole-embryo spatiotemporal modeling. Its advanced features include: • 3D alignment and reconstruction at the whole-mouse-embryo scale (see the animation). • 3D spatial domain digitization and cell-cell communication analysis to understand spatial gene expression gradients and both inter- and intracellular communication. • 3D morphometric and volumetric analyses along with 3D morphogenesis vector field modeling to quantify dynamics such as surface area, volume, and cell density across organs, and to dissect the interplay between morphogenesis factors and cell migration. • A “Google Earth”-like browser, Spateo-viewer ( and for interactive and intuitive exploration of 3D spatial data. • Additional features, such as RNA signal-based single-cell segmentation. We are also honored that Nature “News and Views” has highlighted this work as well: This is really an amazing outcome after two years' heroic revision process that rewrite the entire paper using a new data ( for whole mouse embryos.

We are thrilled to share that our first paper from my new lab, Spateo ( for spatiotemporal modeling of molecular holograms, is now online in Cell: Spateo is a comprehensive analytical framework for 3D whole-embryo spatiotemporal modeling. Its advanced features include: • 3D alignment and reconstruction at the whole-mouse-embryo scale (see the animation). • 3D spatial domain digitization and cell-cell communication analysis to understand spatial gene expression gradients and both inter- and intracellular communication. • 3D morphometric and volumetric analyses along with 3D morphogenesis vector field modeling to quantify dynamics such as surface area, volume, and cell density across organs, and to dissect the interplay between morphogenesis factors and cell migration. • A “Google Earth”-like browser, Spateo-viewer ( and for interactive and intuitive exploration of 3D spatial data. • Additional features, such as RNA signal-based single-cell segmentation. We are also honored that Nature “News and Views” has highlighted this work as well: This is really an amazing outcome after two years' heroic revision process that rewrite the entire paper using a new data ( for whole mouse embryos.

evo-devo

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Museum curators faced with cleaning animal skeletons for display may soon turn to an unusual new tool: flesh-eating beetle larvae known as “superworms.” These superworms can clean up an animal carcass in a matter of hours or days while keeping the bones intact, researchers report. Learn more: News from Science

Museum curators faced with cleaning animal skeletons for display may soon turn to an unusual new tool: flesh-eating beetle larvae known as “superworms.” These superworms can clean up an animal carcass in a matter of hours or days while keeping the bones intact, researchers report. Learn more: News from Science

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⚡️📣👇Tremendously excited to share our new Cell article, where we develop TriPath, a method for analyzing 3D pathology samples using weakly supervised AI. Article: TriPath enables 3D computational pathology via 3D multiple instance learning allowing AI models to capture intricate morphological details from pathology volumes. Code: Blog post: Tested on two different imaging modalities, and patient cohorts from two institutions. Our superstar Andrew H. Song put in a monumental effort of leading the study, in a fantastic collaboration with Jonathan Liu at University of Washington . Interesting aspects: - Utilizing the whole tissue volume and leveraging 3D deep learning enable superior risk prediction performance compared to 2D deep learning baselines based on a few sampled tissue sections that emulate standard clinical practice. This indicates TriPath can harness additional information provided by 3D tissue morphology. - The performance is also superior to clinical baselines from a reader study that involved six expert pathologists. - The morphologically heterogeneous tissue volume could lead to opposing patient-level outcome predictions, dependent on which portion of the tissue volume is used. This concurs with current clinical literature warning that tissue sampling bias can lead to misdiagnosis. Some limitations: - While the 3D pathology cohort size is unprecedented, it is smaller than typical 2D pathology cohorts. Further large-scale studies will be required for validation. Nevertheless, we believe that this study will initiate a positive cycle, encouraging academic institutions and pharmaceutical companies to contribute large banks of human tissue blocks with paired clinical outcomes, thus speeding up advancements in 3D computational pathology. Concluding insights: We believe that 3D pathology is just around the corner - It has the huge potential to not only augment/improve the current clinical practice centered around 2D examination of human tissue, but also help reveal novel biomarkers for prognosis and therapeutic response.. Harvard Medical School Harvard Data Science Initiative Mass General Brigham Broad Institute

⚡️📣👇Tremendously excited to share our new Cell article, where we develop TriPath, a method for analyzing 3D pathology samples using weakly supervised AI. Article: TriPath enables 3D computational pathology via 3D multiple instance learning allowing AI models to capture intricate morphological details from pathology volumes. Code: Blog post: Tested on two different imaging modalities, and patient cohorts from two institutions. Our superstar Andrew H. Song put in a monumental effort of leading the study, in a fantastic collaboration with Jonathan Liu at University of Washington . Interesting aspects: - Utilizing the whole tissue volume and leveraging 3D deep learning enable superior risk prediction performance compared to 2D deep learning baselines based on a few sampled tissue sections that emulate standard clinical practice. This indicates TriPath can harness additional information provided by 3D tissue morphology. - The performance is also superior to clinical baselines from a reader study that involved six expert pathologists. - The morphologically heterogeneous tissue volume could lead to opposing patient-level outcome predictions, dependent on which portion of the tissue volume is used. This concurs with current clinical literature warning that tissue sampling bias can lead to misdiagnosis. Some limitations: - While the 3D pathology cohort size is unprecedented, it is smaller than typical 2D pathology cohorts. Further large-scale studies will be required for validation. Nevertheless, we believe that this study will initiate a positive cycle, encouraging academic institutions and pharmaceutical companies to contribute large banks of human tissue blocks with paired clinical outcomes, thus speeding up advancements in 3D computational pathology. Concluding insights: We believe that 3D pathology is just around the corner - It has the huge potential to not only augment/improve the current clinical practice centered around 2D examination of human tissue, but also help reveal novel biomarkers for prognosis and therapeutic response.. Harvard Medical School Harvard Data Science Initiative Mass General Brigham Broad Institute

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⚡🎉 We are thrilled to introduce VORTEX, an AI-powered computational framework for predicting 3D Spatial Transcriptomics (ST) using 3D tissue images and minimal 2D ST! 🧬 By combining cutting-edge 3D non-destructive tissue imaging with AI, VORTEX imputes the 3D molecular landscape of large tissue samples in a cost-effective and scalable manner. 🧠💡Our approach: By pretraining on diverse 3D morphology–2D transcriptomic pairs from heterogeneous tissue samples, and then fine-tuning on minimal 2D ST data from a volume of interest, VORTEX leverages both generic tissue-specific and sample-specific morphomolecular correlates to predict 3D ST. Congratulations to our superstar co-leads Cristina Almagro Pérez and Andrew H. Song, this was an exciting collaboration with Jonathan Liu Sizun Jiang Ali Bashashati. Preprint: Demo: Read the excellent blog from our superstar grad student Cristina Almagro Pérez: Also see our previous work on 3D Computational Pathology from Andrew H. Song published in Cell last year: Stay tuned for more to come.

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Ali Max Erturk

14,781 просмотров • 8 месяцев назад

GaVS: 3D-Grounded Video Stabilization via Temporally-Consistent Local Reconstruction and Rendering Contributions: • We reformulate video stabilization as a novel 3D grounded scheme of local reconstruction and rendering. This approach is naturally robust to diverse camera motions and scene dynamics, is temporally consistent, and is capable of full frame stabilization. • We propose a novel test-time optimization for each unstable video. It leverages multi-view dynamics-aware photometric supervision and cross-frame regularization to achieve temporally consistent reconstructions. To avoid frame cropping, we introduce a scene extrapolation module based on video completion. • We provide a 3D-grounded dataset for our task by re-purposing an existing one, and introduce new metrics on sparse and dense reconstruction to evaluate 3D scene consistency. Extensive experiments (quantitative, qualitative, user study) versus image-based and gyro-basedmethods demonstrate the merits of our method.

GaVS: 3D-Grounded Video Stabilization via Temporally-Consistent Local Reconstruction and Rendering Contributions: • We reformulate video stabilization as a novel 3D grounded scheme of local reconstruction and rendering. This approach is naturally robust to diverse camera motions and scene dynamics, is temporally consistent, and is capable of full frame stabilization. • We propose a novel test-time optimization for each unstable video. It leverages multi-view dynamics-aware photometric supervision and cross-frame regularization to achieve temporally consistent reconstructions. To avoid frame cropping, we introduce a scene extrapolation module based on video completion. • We provide a 3D-grounded dataset for our task by re-purposing an existing one, and introduce new metrics on sparse and dense reconstruction to evaluate 3D scene consistency. Extensive experiments (quantitative, qualitative, user study) versus image-based and gyro-basedmethods demonstrate the merits of our method.

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