============ notebook changes: - change nan-dropping to only apply to all-nan rows in final dataframe - include more image intensity metric earlier in trajectory step - remove minSize from masking process - thresholdWindow and bgWindow now denote number of frames used for estimation
main module: - update watershed for collision handling to apply dilations (create areas similar to mask process)
0.91
============ notebook changes: - unified setup function to create all paths and logger etc - updated runscript for parallel submission includes a 'dry-run'
main module: - improved robustness to other imaging setups including different depth, scalings - include adaptive peak detection
0.9
============ notebook changes: - unified function for running n=1 workers or more - separate dataframe and images - save images for each worm separately
main module changes: - unified parallelization to one function util. for feature detection and the full pharaglow extraction - remove now-redundant functions in tracking code - rewrite runPharaglowOnStack to avoid using apply