Segmentation Module

Synapses Segmentation

The Segmentation Module employs image processing techniques to delineate synapses within volumetric datasets, with additional methods planned for future implementation. It includes tools for executing segmentation tasks and recording the coordinates of each identified synapse.

exr.segmentation.segmentation.synapses_roi_segmentation(config, round, roi, channel, top_intensity_percentage=3, size_thershold=3500, dilate_erode_iteration=2)[source]

Segment synapses in a specific ROI (Region Of Interest) and round using various image processing steps.

Parameters:

  • config (Config) – Configuration options. This should be an instance of the Config class.

  • round (int) – The round to segment.

  • roi (int) – Region of interest to segment.

  • channel (str) – The channel to segment.

  • top_intensity_percentage (int) – The top intensity percentage for thresholding. Default is top 3%.

  • size_thershold (int) – The size threshold for instance segmentation. Default is 3500.

  • dilate_erode_iteration (int) – Number of dilate and erode iterations. Default is 2.

Raises:

Raises an exception if an error occurs during the segmentation process.

Note:

The results are saved to a TIFF file located at <roi_analysis_path>/segmentation_masks.

Return type:

None