Datasets

All data used for training and validation of DeepCAD-RT are made publicly available here. Experimentally obtained data were captured by our two-photon imaging system composed of (1) a standard two-photon microscope with multi-color detection capability and (2) a customized two-photon microscope with two strictly synchronized detection paths. The signal intensity of the high-SNR path is 10-fold higher than that of the low-SNR path. We provide 11 groups of data (~250 GB), including synthetic calcium imaging data; recordings of in vivo calcium dynamics in mice, zebrafish and flies; 2D and 3D imaging of neutrophil migration; 2D and 3D imaging of mouse cortical ATP release. All data are listed in the table below and we have no restriction on data availability. You can download these data by clicking the DOI hyperlinks appended in the ‘Title’ column. We recommend using ImageJ/Fiji to open and view these files.

No. Title Events Pixel size Frame/volume rate Imaging Depth* Data size Comments
1
Synthetic calcium imaging dataDOI
 Calcium transient 1.020 μm/pxl 30 Hz 200 μm 29.8 GB Low-SNR/high-SNR
2
Mouse dendritic spines DOI
 Calcium transient 0.155 μm/pxl 30 Hz 40 μm 21.7 GB Low-SNR/high-SNR
3
Zebrafish optic tectum neuronsDOI
 Calcium transient 0.254 μm/pxl 30 Hz —— 6.3 GB Low-SNR/high-SNR
4
Zebrafish multiple brain regionsDOI
 Calcium transient 0.873 μm/pxl 15 Hz —— 7.2 GB Low-SNR/high-SNR
5
Drosophila mushroom bodyDOI
 Calcium transient 0.254 μm/pxl 30 Hz —— 11.1 GB Low-SNR/high-SNR
6
Mouse brain neutrophilsDOI
 Cell migration 0.349 μm/pxl 10 Hz 30 μm 11.8 GB Low-SNR/high-SNR
7
Mouse brain neutrophils (3D)DOI
 Cell migration 0.310 μm/pxl 2 Hz 15-45 μm (2 μm/ plane) 27.4 GB Low-SNR, 2 colors
8
ATP release in the mouse brainDOI
 ATP dynamics 0.465 μm/pxl 15 Hz 20 μm 6.0 GB Low-SNR/high-SNR
9
ATP release in the mouse brain (3D) DOI
ATP dynamics 0.698 μm/pxl 1 Hz 10-70 μm (2 μm/plane) 50.2 GB Low-SNR
10
Mouse neurites DOI
 Calcium transient 0.977 μm/pxl 30 Hz 40-80 μm 23.5 GB Low-SNR/high-SNR
11
Mouse neuronal populationsDOI
Calcium transient 0.977 μm/pxl 30 Hz 90-180 μm 53.6 GB Low-SNR/high-SNR 
*Depth: imaging depth below the brain surface. Only for mouse experiments.

Citation

If you use these datasets, please cite the companion paper:

Xinyang Li, Yixin Li, Yiliang Zhou, et al. Real-time denoising enables high-sensitivity fluorescence time-lapse imaging beyond the shot-noise limit. Nat Biotechnol (2022). https://doi.org/10.1038/s41587-022-01450-8