Dataset of Axon Segmentation and Centerlines, Acquired using a Two-photon Microscope in the Live Mouse Cortex

This dataset contains 20 images of real axons that were published previously in Bass et al (2017). This subset dataset has been added labels of binary images for segmentation of the axons, and of centerline for tracing of the axons.

We provide the following:

• Images-MAX: 2D images of axons (.png)
• Images-TIFF: 3D images of axons (.tiff)
• Labels-binary: Manual segmentation of the axons as binary images (.png)
• Labels-tracing: Manual tracing of the axons (.swc)

This data was collected in the live mouse cortex, using a two-photon microscope, with a 40x objective, at zoom 4, and with a resolution of 512 × 512 pixels, 0.147 μm per pixel for the x, y planes, and 1 μm for the z plane. . 

Please cite the following papers when using this dataset:

T. Dai, M. Dubois, K. Arulkumaran, J. Campbell, B. Billot, C. Bass, Z. Uslu, V. De Paola, C. Clopath, and A. A. Bharath. Deep reinforcement learning for subpixel neural tracking. Medical Imaging with Deep Learning. 2019.

Bass C, Helkkula P, De Paola V, Clopath C, Bharath AA. Detection of axonal synapses in 3D two-photon images. Giniger E, ed. PLoS ONE. 2017;12(9):e0183309. doi:10.1371/journal.pone.0183309.