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12-15 August 2018
Europe/Berlin timezone

Mastodon -- a large-scale track-editing framework for light sheet data

14 Aug 2018, 09:00


Pfotenhauerstraße 108 01307 Dresden Germany
Short Talk Light sheet fluorescence microscopy Sample preparation, clearing and expansion


Tobias Pietzsch (MPI-CBG)


Light sheet microscopy allows live 3D imaging of entire developing embryos with
high spatial and temporal resolution. Computational analysis of these recordings
promises new insights in developmental biology. However, a single dataset often
comprises many terabytes, which makes storage, processing, and visualization of
the data a challenging problem. The open-source Fiji platform provides tools to
address this challenge. In this talk, I will present Mastodon, a track-editing
framework for cell tracking and lineage tracing in Fiji.

Large-scale automated tracking in biological datasets is a very active field of
research. To support machine learning methods, editing tools are needed to
facilitate curation, proof-reading, and the manual generation of ground truth
data. To make such tools accessible to biologist researchers, they should be
easy to obtain, learn, and use. Additionally they must be intuitively usable and
remain responsive in the face of millions of tracked objects and terabytes of
image data. To make them useful for researchers in automated tracking, they need
to be open source, adaptable, and extensible. Mastodon is our effort to provide
such a tool in Fiji.

Affiliation MPI-CBG
Terms and Conditions Yes

Primary authors

Tobias Pietzsch (MPI-CBG) Jean-Yves Tinevez (Image Analysis Hub - Citech - Institut Pasteur)

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