Output#

When running the complete analysis in a standard way, these are the various outputs that you will find in the analysis folder:

The results of the analysis are saved in the following way:

  • Segmentation images are saved in the segmented folder as segmented_k_0.tif, segmented_k_1.tif etc. Those images are labeled masks, i.e. each cell gets one label.

  • Tracking information is saved as binary images where only the selected cell appear. Images are called tracked_k_0.tif, tracked_k_1.tif etc.

  • The rasterized cell contours where pixel values correspond to curvilinear distance are stored as 32-bits images rasterized_k_0.tif, rasterized_k_1.tif etc.

  • The binary window images with window boundaries are stored as window_image_k_0.tif, window_image_k_1.tif etc.

  • The list of pixel indexes indicating to which window each pixel belongs are stored as pickle files window_k_0.pkl, window_k_1.pkl etc.

  • Other information such as spline functions are stored in a pickled Results.pkl file.

  • Parameters of the experiments are saved in a human readable Parameters.yml file.