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Here are the counts I get with the script, which are different from the google sheets.

M_AMD_000058_L                                                                                                                                          
SGN                                                                                                                                                     
Number of SGNs (all components)   : 25061                                                                                                               
Number of SGNs (largest component): 17269                                                                                                               
M_LR_000144_L                                                                                                                                           
SGN                                                                                                                                                     
Number of SGNs (all components)   : 11502                                                                                                               
Number of SGNs (largest component): 5132                                                                                                                
M_LR_000145_L                                                                                                                                           
SGN                                                                                                                                                     
Number of SGNs (all components)   : 9776                                                                                                                
Number of SGNs (largest component): 4212                                                                                                                
M_LR_000151_R                                                                                                                                           
SGN                                                                                                                                                     
Number of SGNs (all components)   : 13921                                                                                                               
Number of SGNs (largest component): 8613                                                                                                                
M_LR_000155_L                                                                                                                                           
SGN                                                                                                                                                     
Number of SGNs (all components)   : 12478                                                                                                               
Number of SGNs (largest component): 9264                                                                                                                
M_LR_000167_R                                                                                                                                           
SGN                                                                                                                                                     
Number of SGNs (all components)   : 11591                                                                                                               
Number of SGNs (largest component): 11484                                                                                                               
SGN_resized                                                                                                                                             
Number of SGNs (all components)   : 14311                                                                                                               
Number of SGNs (largest component): 11592                                                                                                               
M_LR_000184_L                                                                                                                                           
SGN                                                                                                                                                     
Number of SGNs (all components)   : 22099                                                                                                               
Number of SGNs (largest component): 10998 

@constantinpape constantinpape marked this pull request as ready for review May 9, 2025 08:27
@constantinpape
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@schilling40 : this is ready now. It contains a (parallelized) implementation for intensity and volume measurements that should work with segmentations in MoBIE format (= ome.zarr + the table). The relevant functions are flamingo_tools.measurement.compute_object_measures (for a segmentation stored on disc) and flamingo_tools.measurement.compute_object_measures_impl (for a segmentation passed as numpy array).

This is the functionality we will use for the first SGN + GFP measurements.

The rest of the changes are just some improved tests, doc strings, and scripts that segment the new data from Aleyna and then apply these measurements.

If you have time you could have a short look if everything makes sense. I will then merge it later.

@constantinpape constantinpape merged commit aee6121 into master May 14, 2025
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@constantinpape constantinpape deleted the measurements branch May 14, 2025 09:15
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2 participants