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Bioimage Annotations

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Bioimage Annotations
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Research at Janelia using advanced imaging techniques at the light or ultrastructural level produces large amounts of image data that often require manual annotation or curation for further analysis. Such annotations are also required to create ground truth data for machine learning with the goal to automate image processing at scale.

PTR staff assigned to the MouseLight team project reconstructs the axonal harbors of individual neurons across the mouse brain. We also collaborate with many Janelia labs in support of various annotation efforts, such as

(Fluorescence microscopy image volumes)

  • 3D annotations of fluorescently labeled neurons in images of the fly central nervous system (e.g. of lines in the Split-GAL4 driver collection), often to correlate with neurons in EM images, such as the fly Hemibrain.
  • 3D annotations of fluorescently labeled cells (nuclei) or organs in larval zebrafish for machine learning (Ahrens lab)
  • 4D light level annotations of nuclei in the developing C. elegans embryos to interrogate the cell positions and dynamics over time (Shroff lab).

(Ultrastructural image volumes)

  • Annotation of structures in microCT images using VVD viewer.
  • Voxel-based annotations of cell bodies in FIB SEM volumes (FIB SEM Technology) using Amira software.

For voxel-based annotations we often leverage the knowledge accrued by the CellMap team, who is training PTR members as needed. Typically, such annotations are used to establish machine learning algorithms to automate cell or organelle segmentations.

(Behavior videos)

  • Animal part tracking using the APT software developed by Kristen Branson to annotate videos of animal behavior (Fruit fly, mouse, rat). These data may be utilized to inform biomechanical models or to study the neuronal control of behavior.


Spike sorting curation

In addition to image annotations, several members of the PTR team are trained in the curation of electrophysiology data recorded from multi-site electrodes (e.g. Neuropixels) and analyzed using software such as Kilosort (Pachitariu and Stringer labs). This is a collaboration with the Harris lab.