Super-Segger-Toolkit

Toolkit for linking cells from masks matrix, providing the empty graph to be filled in, and visualization tools like lineage, phase image.

The main idea is to store the linking result as a Graph of Cells:

• Class Cell:
  • self.frame
  • self.label
  • self.polygon
• Class Graph:
  • self.node
  • self.edge: (node, node)

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The main data resource manager, called LinkComposer, stores phase/mask directories and cells set. It helps in quickly plotting information.

Steps:

1. Create a LinkComposer:
   • LinkComposer.read_folder(mask_folder, phase_folder)
   • LinkComposer.read_tif(mask_tif, phase_tif)
2. Ask composer for an empty directed graph: composer.make_new_directed_graph()
3. Fill in edges on the tree: composer.link(G, cell1, cell2)
4. Check results by visualization:
   • visualizer.quick_lineage(G)
   • visualizer.get_label_info(G), composer.show_frame_phase(...)
5. Finished. Also, multiple linker comparisons can be done, if desired.

Read Demo for more information:

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Visualization:

Notice although the following data are all in group of three, they are not related to each other, I choice num=3 for each sample just because it looks nice in that way.

1. Phase tracking videos: Cell Event Tracking Labeling: check different label demo for more information.

Cell Event Tracking Labeling: check different label demo for more information.

• Cell Event Tracking labeling

2. Cross time phase video compasion:

Also, check demo visualization for more information

3. Lineage comparsion:

Check demo visualization for more information, this lineage is from falimented cells rather than above data, since this data lineage is more interesting and falimented cells phase data more interesting, so using different data on different visualization.

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