BioTISR: a time-lapse biological image dataset for super-resolution microscopy

<p>BioTISR is a biological image dataset for super-resolution microscopy, currently including 2D and 3D time-lapse image pairs of low-and-high resolution images of a variety of biology structures, aiming to provide a high-quality dataset of time-lapse biological SR images for the community to spark more developments of computational SR methods.</p> <p>At present, 2D dataset includes five specimens (clathrin-coated pits, lysosomes, outer mitochondrial membrane, microtubules, and F-actin) acquired with the GI/TIRF-SIM mode and nonlinear SIM mode of our Multi-SIM system, and 3D dataset includes three specimens (outer mitochondrial membrane, microtubules, and F-actin) acquired with 3D-SIM mode of the Multi-SIM system. For each type of specimen and each imaging modality, we acquired the raw data from at least 50 distinct regions-of-interest (ROI). For each ROI, we acquired two (3D data) or three (2D data) groups of N-phase &times; M-orientation &times; T-timepoint raw images with a constant exposure time but increasing the excitation light intensity, where (N, M, T) are (3, 3, 20) for TIRF-SIM and GI-SIM, (5, 5, 10) for nonlinear SIM, and (3, 5, 10) for 3D-SIM. Specific imaging conditions and scripts for reading MRC file are provided in Supplement Files.</p> <p>The BioTISR dataset is related to the following paper:<a href="https://www.nature.com/articles/s41587-025-02553-8#citeas">Qiao, C., Liu, S., Wang, Y.&nbsp;<em>et al.</em>&nbsp;A neural network for long-term super-resolution imaging of live cells with reliable confidence quantification.&nbsp;<em>Nat Biotechnol</em> (2025). https://doi.org/10.1038/s41587-025-02553-8</a>, which is an extension of our previously published <a href="https://doi.org/10.6084/m9.figshare.13264793.v9">BioSR dataset</a> (https://www.nature.com/articles/s41592-020-01048-5).</p> <p>Limited by quota, the original images uploaded in the current 3D dataset are wide-field images obtained after averaging 15 images, where (N, M, T) are (1, 1, 10). We will update them to raw SIM images after the quota is expanded.</p> <p>2D dataset's url:</p> <p><a href="https://doi.org/10.5281/zenodo.13843670" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.13843670</a></p> <p>3D dataset's urls:</p> <p>F-actin:</p> <p>WF input: <a href="https://doi.org/10.5281/zenodo.13843673">https://doi.org/10.5281/zenodo.13843673</a></p> <p>Raw SIM input:<a href="https://doi.org/10.5281/zenodo.13994464" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.13994464</a></p> <p>Microtubules:</p> <p>WF input:&nbsp;<a href="https://doi.org/10.5281/zenodo.13932988" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.13932988</a></p> <p>Raw SIM input: <a href="https://doi.org/10.5281/zenodo.13989327" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.13989327</a></p> <p>Mitochondria:</p> <p>WF input: <a href="https://doi.org/10.5281/zenodo.13843183" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.13843183</a></p> <p>Raw SIM input: <a href="https://doi.org/10.5281/zenodo.14000502" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.14000502</a></p> <p>&nbsp;</p> <p>Update 2025.5.6</p> <p>Add optical transfer function(OTF) of the microscopy system and the pixel size of each data to the supplementary files.</p>