Datasets
We share microscopy datasets, trained models and other research data from our work. Many accompany published papers or provide examples for our image-analysis tools. Looking for analysis software? See our software.
Image data
- Data associated with "Pancreatic cancer cells breach endothelial barriers through protrusion-driven invasion or endothelial retraction"
Dataset associated with the bioRxiv preprint “Pancreatic cancer cells breach endothelial barriers through protrusion-driven invasion or endothelial retraction.”
2026 · Paper: bioRxiv · 2026Open access
- Fast label-free live imaging with FlowVision reveals key principles of cancer cell arrest on endothelial monolayers
This repository contains all the data used to make the figure shown in the paper
2026 · Paper: The EMBO Journal · 2026Open access
- Filopodia-mediated trans-endocytosis dataset
This repository contains the raw image and numerical data used to make the figures shown in the preprint.
2026 · Paper: bioRxiv · 2026Open access
- NucleiSky enables cross-scale multimodal registration of microscopy data using nuclei constellations
Dataset associated with the NucleiSky preprint.
2026 · doi:10.5281/zenodo.20721416 · Paper: Journal of Cell Science · 2026Open access
- Filopodome proteomics dataset
This repository contains all the data used to make the figures shown in the paper.
2025 · Paper: Current Biology · 2019Open access
- Immune cells perfusion CD44 Blocking Antibody and Il1b 2h and 16h tracking dataset
Tracking results for mononucleated cells and neutrophils perfused on endothelial monolayers with/without IL-1β and CD44 blocking antibody.
2025 · doi:10.5281/zenodo.17159634 · Paper: The EMBO Journal · 2026Open access
- NanoPyx - Figures' Data
NanoPyx - Figures’ Data
2025 · Paper: Nature Methods · 2025Open access
- PhotoFiTT: A Quantitative Framework for Assessing Phototoxicity in Live-Cell Microscopy Experiments
This repository contains all the data related to the study PhotoFiTT (Phototoxicity Fitness Time Trial) as well as example data for PhotoFiTT computational framework
2025 · Paper: Nature Communications · 2025Open access
- SReD - Figure's data
This repository contains all the data related to the SReD paper
2025 · doi:10.5281/zenodo.13764726 · Paper: Nature Communications · 2025Open access
- CD44 Blocking Antibody perfusion tracking dataset
Tracking dataset used to analyze attachment of PDAC cells to endothelium with CD44 blocking antibody treatment.
2024 · Paper: The EMBO Journal · 2026Open access
- CellTracksColab - breast cancer cell dataset
Dataset used in the manuscript “CellTracksColab—A platform for compiling, analyzing, and exploring tracking data”
2024 · Paper: PLOS Biology · 2024Open access
- CellTracksColab - Filopodia dataset
Dataset used in the manuscript “CellTracksColab—A platform for compiling, analyzing, and exploring tracking data”
2024 · Paper: PLOS Biology · 2024Open access
- CellTracksColab - T cell dataset (full)
Dataset used in the manuscript “CellTracksColab—A platform for compiling, analyzing, and exploring tracking data”
2024 · Paper: PLOS Biology · 2024Open access
- HUVEC CD44 siRNA perfusion tracking dataset
Tracking dataset used to analyze attachment of PDAC cells to endothelium under endothelial CD44 siRNA perturbation.
2024 · Paper: The EMBO Journal · 2026Open access
- Hyaluronidase treatment perfusion tracking dataset
Tracking dataset used to analyze attachment of PDAC cells to endothelium after hyaluronidase treatment.
2024 · Paper: The EMBO Journal · 2026Open access
- PDAC cells CD44 siRNA perfusion tracking dataset
Tracking dataset used to analyze attachment of PDAC cells to endothelium under CD44 siRNA perturbation.
2024 · Paper: The EMBO Journal · 2026Open access
- PDAC cells vs Immune cells perfusion tracking dataset
Tracking dataset used to analyze attachment of PDAC and immune cells to endothelium.
2024 · Paper: The EMBO Journal · 2026Open access
- pix2pix_HUVEC_juctions_dataset
Artificial labeling model used to label cell-cell junctions from brightfield images with endothelial and immune/cancer cells.
2024 · Brightfield · SSIM 0.270, LPIPS 0.360 · Paper: The EMBO Journal · 2026Open access
- pix2pix_HUVEC_nuclei_cancer_cells_dataset
Artificial labeling model used to label nuclei from brightfield images containing cancer and endothelial cells.
2024 · Brightfield · SSIM 0.755, LPIPS 0.120 · Paper: The EMBO Journal · 2026Open access
- pix2pix_HUVEC_nuclei_immuno_cells_dataset
Artificial labeling model used to label nuclei from brightfield images containing immune and endothelial cells.
2024 · Brightfield · SSIM 0.756, LPIPS 0.130 · Paper: The EMBO Journal · 2026Open access
- StarDist_AsPC1_Lifeact
StarDist model for segmenting AsPC1 cells from LifeAct channel, including single-cell separation from clusters.
2024 · Fluorescence · IoU 0.884, F1 0.967 · doi:10.5281/zenodo.13442128 · Paper: The EMBO Journal · 2026Open access
- StarDist_BF_cancer_cell_dataset_10x
StarDist model for segmenting cancer cells on endothelial cells at 10x magnification.
2024 · Brightfield · IoU 0.882, F1 0.968 · doi:10.5281/zenodo.13304399 · Paper: The EMBO Journal · 2026Open access
- StarDist_BF_cancer_cell_dataset_20x
StarDist model for segmenting cancer cells on endothelial cells at 20x magnification before tracking.
2024 · Brightfield · IoU 0.793, F1 0.921 · Paper: The EMBO Journal · 2026Open access
- StarDist_BF_Monocytes_dataset
StarDist model for segmenting mononucleated cells on endothelial cells prior to tracking.
2024 · Brightfield · IoU 0.831, F1 0.941 · Paper: The EMBO Journal · 2026Open access
- StarDist_BF_Neutrophil_dataset
StarDist model for segmenting neutrophils on endothelial cells prior to tracking.
2024 · Brightfield · IoU 0.914, F1 0.969 · Paper: The EMBO Journal · 2026Open access
- StarDist_Fluorescent_cells
StarDist model to detect cancer cells from fixed fluorescence samples for attached-cell quantification.
2024 · Fluorescence · IoU 0.646, F1 0.877 · Paper: The EMBO Journal · 2026Open access
- StarDist_HUVEC_nuclei_dataset
StarDist model for segmenting endothelial nuclei while ignoring cancer cells.
2024 · Fluorescence · IoU 0.927, F1 0.976 · Paper: The EMBO Journal · 2026Open access
- Stardist_MiaPaCa2_from_CD44
StarDist model for segmenting MiaPaCa2 cells from the CD44 channel while ignoring endothelial cells.
2024 · Fluorescence · IoU 0.884, F1 0.950 · Paper: The EMBO Journal · 2026Open access
- StarDist_TumorCell_nuclei
StarDist model for segmenting tumor cell nuclei while ignoring endothelial nuclei.
2024 · Fluorescence · IoU 0.558, F1 0.793 · Paper: The EMBO Journal · 2026Open access
- TLNRD1 figures
Raw microscopy images used to make the figures displayed in the article “TLNRD1 is a CCM complex component and regulates endothelial barrier integrity.”
2024 · Paper: Journal of Cell Biology · 2024Open access
- eSRRF - Supplementary Data
eSRRF datasets used in the manuscript
2023 · doi:10.5281/zenodo.8325164 · Paper: Nature Methods · 2023Open access
- Fast4DRegistration
Data used in the manuscript
2023 · Paper: Journal of Cell Science · 2023Open access
- Training dataset for Fast4DReg workshop
Fast4DReg workshop data
2023 · doi:10.5281/zenodo.8347798 · Paper: Journal of Cell Science · 2023Open access
- Cancer cell migration followed with TrackMate
Dataset of migrating breast cancer cells for analysis with TrackMate. tutorial.
2022 · Paper: Nature Cell Biology · 2021Open access
- Cancer cell migration followed with TrackMate
Stardist model and training dataset for automated tracking of MDA-MB-231 and BT20 cells
2022 · doi:10.5281/zenodo.4812018 · Paper: Nature Cell Biology · 2021Open access
- Cell migration with ERK signalling
Movie following cells expressing ERK and a nuclei staining, tracked with TrackMate and later analyzed with MATLAB.
2022 · Paper: Nature Methods · 2022Open access
- Quantitative comparison of tracking performance using TrackMate-Helper.
we used TrackMate-Helper to assess the performance of TrackMate on four datasets that cover a wide range of biological and imaging situations
2022 · Paper: Nature Methods · 2022Open access
- Segmenting cells in a spheroid in 3D using 2D StarDist within TrackMate
Dataset for segmenting cells in a 3D spheroid using 2D StarDist in TrackMate.
2022 · Paper: Nature Methods · 2022Open access
- T cells migration followed with TrackMate
Dataset of T cells migrating on ICAM-1, tracked using StarDist in TrackMate.
2022 · Paper: Nature Methods · 2022Open access
- Tracking breast cancer cells migrating collectively with TrackMate-Cellpose
Dataset for tracking collective migration of breast cancer cells with TrackMate-Cellpose.
2022 · Paper: Nature Methods · 2022Open access
- Tracking cell migration with the TrackMate threshold detector
Dataset used in a tutorial on using the TrackMate threshold detector.
2022 · Paper: Nature Methods · 2022Open access
- Tracking focal adhesions with TrackMate and Weka - tutorial dataset 1
Dataset of MDA-mb-231 cells expressing GFP-paxillin for tracking focal adhesions.
2022 · Paper: Nature Methods · 2022Open access
- Tracking focal adhesions with TrackMate and Weka - tutorial dataset 2
Dataset of human dermal microvascular blood endothelial cells for tracking focal adhesions.
2022 · Paper: Nature Methods · 2022Open access
- Tracking Glioblastoma-astrocytoma cells with TrackMate-Cellpose
Dataset of Glioblastoma-astrocytoma U373 cells migrating on a polyacrylamide gel.
2022 · Paper: Nature Methods · 2022Open access
- Tracking label images with TrackMate
Dataset used in a tutorial on tracking label images with TrackMate.
2022 · Paper: Nature Methods · 2022Open access
- Tracking with TrackMate using mask images of cell migration
Dataset used in a tutorial on tracking mask images with TrackMate.
2022 · Paper: Nature Methods · 2022Open access
- ZeroCostDL4Mic - CARE (2D) example training and test dataset
Paired microscopy images (fluorescence) of low and high signal-to-noise ratio
2021 · doi:10.5281/zenodo.3713330 · Paper: Nature Communications · 2021Open access
- ZeroCostDL4Mic - CARE (3D) example training and test dataset
3D paired microscopy images (fluorescence) of low and high signal-to-noise ratio
2021 · Paper: Nature Communications · 2021Open access
- ZeroCostDL4Mic - CycleGAN example training and test dataset
Unpaired microscopy images (fluorescence) of microtubules (Spinning-disk and SRRF reconstructed images)
2021 · Paper: Nature Communications · 2021Open access
- ZeroCostDL4Mic - DeepSTORM training and example dataset
Experimental time-series dSTORM acquisition of Glial cells stained with phalloidin for actin
2021 · Paper: Nature Communications · 2021Open access
- ZeroCostDL4Mic - Label-free prediction (fnet) example training and test dataset
Hela labeled with TOM20
2021 · Paper: Nature Communications · 2021Open access
- ZeroCostDL4Mic - Noise2Void (2D) example training and test dataset
U-251 glioma cells, endogenously expressing paxillin-GFP
2021 · Paper: Nature Communications · 2021Open access
- ZeroCostDL4Mic - Noise2Void (3D) example training and test dataset
A2780 ovarian carcinoma cells, transiently expressing Lifeact-RFP
2021 · Paper: Nature Communications · 2021Open access
- ZeroCostDL4Mic - pix2pix example training and test dataset
Paired microscopy images (fluorescence) of lifeact-RFP and sir-DNA
2021 · doi:10.5281/zenodo.3941889 · Paper: Nature Communications · 2021Open access
- ZeroCostDL4Mic - Stardist example training and test dataset
DCIS.COM LifeAct-RFP cells stained with SiR-DNA and imaged by spinning-disk confocal microscopy (20x), paired with manually segmented nuclei masks for training StarDist in ZeroCostDL4Mic.
2021 · Paper: Nature Communications · 2021Open access
- ZeroCostDL4Mic - YoloV2 example training and test dataset
MDA-MB-231 cells migrating on cell-derived matrices generated by fibroblasts
2021 · Paper: Nature Communications · 2021Open access
- Combining StarDist and TrackMate example 1 - Breast cancer cell dataset
Contains a StarDist example training dataset, a test dataset, and the StarDist model generated using ZeroCostDL4Mic.
2020 · Paper: F1000Research · 2020Open access
- Combining StarDist and TrackMate example 2 - T cell dataset
Contains a StarDist example training dataset, a test dataset, and the StarDist model generated using ZeroCostDL4Mic.
2020 · Paper: F1000Research · 2020Open access
- Combining StarDist and TrackMate example 3 - Flow chamber dataset
Contains a StarDist example training dataset, a test dataset, and the StarDist model generated using ZeroCostDL4Mic.
2020 · Brightfield · IoU 0.813, F1 0.933 · Paper: F1000Research · 2020Open access
- FiloMap Test Dataset
Dataset for testing and validation in FiloMap for mapping localization of proteins within filopodia from microscopy images.
2019 · Paper: Methods in Molecular Biology · 2023
- S-JCBD-201704045
Raw data from figures
2017 · Paper: Journal of Cell Biology · 2017Open access
- S-JCBD-201302041
Raw data from figures
2013 · Paper: Journal of Cell Biology · 2013Open access
Proteomic data
- MYO10-TurboID in U2-OS and U-87 MG cells
Identification of Myosin-X (MYO10) proximal proteins using TurboID in U2-OS and U-87 MG cells.
2025 · Paper: Journal of Cell Science · 2026Open access
- TLNRD1-GFP Pulldown in HEK293T Cells
Pulldown of human TLNRD1-GFP and GFP in HEK cells for mass spectrometry analysis of binding partners.
2023 · Paper: Journal of Cell Biology · 2024Open access
- Talin1-GFP Pulldown in U2OS Cells
Study of human Talin1-GFP and GFP pulldown from U2OS cells plated on fibronectin, using mass spectrometry.
2021 · Paper: Journal of Biological Chemistry · 2021Open access
- Sharpin-GFP Pulldown in HEK293T Cells
Analysis of human Sharpin-GFP and GFP pulldown from HEK293T cells, identifying binding partners through mass spectrometry.
2017 · Paper: Journal of Cell Science · 2017Open access
- Plasma Membrane, Endosomal, and Cytoplasmic Fractions in Mouse Embryonic Fibroblast
Cellular fractionation experiments to identify novel endosomal proteins in mouse embryonic fibroblast.
2015 · Paper: Nature Cell Biology · 2015Open access
- Proteomic analysis of filamin-A, IQGAP1, Rac1 and RCC2 binding partners
Analysis of human filamin-A-GFP, IQGAP1-GFP, Rac1 and RCC2-GFP and GFP pulldown from HEK293T cells, identifying binding partners through mass spectrometry.
2013 · Paper: Journal of Cell Science · 2013Open access
Sequencing data
- MYO10-Filopodia Breast Tumor Xenograft Expression Dataset
mRNA sequencing data from subcutaneous breast tumor xenografts of MCF10DCIS.com cell lines expressing non-targeting control shRNA (4 tumors) or Myosin-X targeting shRNA (4 tumors).
2022 · Paper: Developmental Cell · 2022Open access