Current pipeline

1. experiment
save into multidimension ND2 files

2. ND2 to tiff files
use either NIS element or NIS element viewer to export ND2 to tiff files
xyt
keep image as multichannel

3. sorting by sorting.py, 
assign the folder where the exported tiff files are.
the python script will sort the files by xy and t, and organize in to folders by xy.

3. Segmentation
Use a modified DeepCell deep learning segmentation to process the sorted files by nested folders.
Just set the top level folder, the script will find all nested folders and process all the files into either binary mask or indexed 8 bit masks.

4. xy tracking by lineage mapper.

5. summarize ROI analysis by feeding the masks into ImageJ and analyze particles.

6. jupyter notebook to process data through panda.

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