skalalab / cell-analysis-tools

Collection of tools used for pre-processing, processing and post processing
GNU General Public License v3.0
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regionprops like function for OMI parameters #7

Closed emmanuel-contreras closed 1 year ago

emmanuel-contreras commented 3 years ago

Creating a function for OMI regionprops would be really useful especially if we can pass in our dictionaries and have it return a dictionary of all the OMI parameters per ROI

Masked array for this implementation would be appropriate to only select those pixels within the mask and not bg

# per roi 
dict_omiprops = {

    # image level
    "number_of_cells" : "",

    #spc exports
    #fad
    "fad_photons_sum" : "", # intensity sum
    "fad_a1" : "", # float
    "fad_a2" : "", # float
    "fad_t1" : "", # float
    "fad_t2" : "", # float
    "fad_tm" : "", # float

    #nadh
    "nadh_photons_sum" : "", # intensity sum
    "nadh_a1" : "", # float
    "nadh_a2" : "", # float 
    "nadh_t1" : "", # float
    "nadh_t2" : "", # float
    "nadh_tm" : "", # float

    #
    "redox_ratio" : "",
    }
emmanuel-contreras commented 2 years ago

add validation to the regionprops a2 + a1 == 100 roi? do bounding box match on each roi?

--------- possible approach for OMI regionprops call regionprops for each image (a1,a2,t1,t2, redox ratio, tm)

return dictionary of 13 parameters mean and stdev

1. nadh_intensity
2. nadh_a1
3. nadh_a2
4. nadh_t1
5. nadh_t2
6. nadh_tau_mean
7. fad_intensity
8. fad_a1
9. fad_a2
10. fad_t1
11. fad_t2
12. fad_tau_mean
13. redox_ratio