Dataset from Cellpose3, two-photon calcium imaging from ribo-gcamp8s-expressing neurons

For testing denoising algorithms, we collected a new dataset of noisy images using in vivo two-photon imaging in mice expressing somatic jGCaMP8s (riboL1-jGCaMP8s mouse line) (Zhang et al, 2023, Wang et al 2023) as described in Stringer et al 2021. We imaged each neural field of view for 300+ time-frames at a frame rate of 30Hz. 12 fields of view had dense expression and 8 fields of view had sparse expression. As ground-truth for the segmentations, we used the average of 300 frames. Based on the average ROI size in the time-averaged image segmentation, we set the diameter to 17 for use for all denoising and segmentation.

If you use this dataset, please cite the Cellpose 3 paper: https://www.biorxiv.org/content/10.1101/2024.02.10.579780v2