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TeraFly: real-time three-dimensional visualization and annotation of terabytes of multidimensional volumetric images

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Figure 1: Overview of TeraFly image and surface-object visualization.

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Acknowledgements

We thank F.S. Pavone, L. Sacconi, L. Silvestri, J.P. Ghobril, R. Tsien, H. Zeng, P. Keller and E. Betzig for providing the data sets we used in this work, as well as for the useful discussions that helped us in the requirement analysis of our tool.

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Supplementary Text

Supplementary Notes 1–7 (PDF 3429 kb)

Supplementary Video 1

Instant three-dimensional visualization of a 0.8-terabyte image. Image: entire brain of a L1-GFP mouse acquired using light sheet microscopy (courtesy of F.S. Pavone, L. Sacconi, L. Silvestri). In this video, the user zooms-in and out with the mouse scroll through all image resolution levels. (AVI 18657 kb)

Supplementary Video 2

Instant three-dimensional visualization of a 110-gigabyte image stored in BigDataViewer HDF5 format. Image: entire cerebellum of a L1-GFP mouse acquired using light sheet microscopy (courtesy of F.S. Pavone, L. Sacconi, L. Silvestri). Compared to Supplementary Video 1, in which the image was stored in TeraFly's format, this video shows again a real-time visualization performance, thus demonstrating that TeraFly does not rely on the optimization of the input data organization. (MP4 40395 kb)

Supplementary Video 3

Three-dimensional proofreading of automatic Purkinje cell counts in a 110-gigabyte image. Image: entire cerebellum of a L1-GFP mouse acquired using confocal light sheet microscopy (courtesy of F.S. Pavone, L. Sacconi, L. Silvestri). In this video, the user first sets up the proofreading session by choosing the volume of interest coordinates, blocks overlap and blocks size and then starts the block-by-block scan. Empty blocks are quickly skipped thanks to a scrollable instant preview of blocks content. Using a series of Virtual Finger-based display and annotation tools, fast and accurate proofreading of cell counts is achieved. (AVI 50063 kb)

Supplementary Video 4

Two-dimensional proofreading of automatic Purkinje cell counts with ImageJ (Cell Counter plugin). Image: 300×300×300 voxels image stack from entire cerebellum of a L1-GFP mouse acquired using light sheet microscopy (courtesy of F.S. Pavone, L. Sacconi, L. Silvestri). Compared to Supplementary Video 2, this video shows the difference in terms of proofreading speed and precision between TeraFly (3D-based) and ImageJ Cell Counter (2D-based). Specifically, here it is more difficult to locate false positives, since markers are too small and overlaid only on a single slice. (AVI 11048 kb)

Supplementary Video 5

Two-dimensional proofreading of automatic Purkinje cell counts with MaMuT/BigDataViewer. Image: 1,020×1,020×1,020 voxels image stack from entire cerebellum of a L1-GFP mouse acquired using light sheet microscopy (courtesy of F.S. Pavone, L. Sacconi, L. Silvestri. Compared to Supplementary Video 2, this video shows the difference in terms of proofreading speed and precision between TeraFly (3D-based) and MaMuT/BigDataViewer (2D-based). Specifically, here the removal of false positives is done slice-by-slice with several user operations, whereas in TeraFly it can be done directly in 3D with just one mouse right-stroke. (MP4 128922 kb)

Supplementary Video 6

Vaa3D-TeraFly-assisted three-dimensional tracing of a rat neuron. Image: rat neuron image acquired using 2-photon microscopy (courtesy of R. Tisen). In this video, the user zooms-in through all image resolution scales to trace neurites of various thickness. (MP4 336820 kb)

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Bria, A., Iannello, G., Onofri, L. et al. TeraFly: real-time three-dimensional visualization and annotation of terabytes of multidimensional volumetric images. Nat Methods 13, 192–194 (2016). https://doi.org/10.1038/nmeth.3767

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