Time Series

PanSeg imports, processes, and exports time series data. In the current version Panseg does not take any advantage of the time data, it only processes the data frame-by-frame. Tracking and other processing across timepoints will be added in a future version.

Supported layouts and formats

The time series layouts are TYX (2D), TZYX (3D), and their multichannel versions TCYX and TCZYX.

Import supports OME-TIFF, h5, and zarr. For OME-TIFF, the input tab prefills the stack layout from the file's OME-XML, and it reads the time spacing from the timing metadata (TimeIncrement or Plane.DeltaT) if the file carries it.

Export writes the time axis back out. Tiff export of a time series is always OME-TIFF, named with the .ome.tiff extension per the OME-TIFF naming convention, with TimeIncrement when the spacing is known. H5 and zarr export carry the layout and the spacing with it.

Limitations

• Training is currently not supported
• Pre- and Postprocessing steps apply to all timepoints.
• Data must fit into memory, but can be truncated during import (see Import)