Morphology Computation

This block is used for extracting morphological features from straightened and unstraightened masks. This block returns a structured CSV (or parquet) file containing all the features extracted for each mask.

Available features¶

• length (requires straightening)

• volume (requires straightening)

• area

• width_mean (requires straightening)

• width_median (requires straightening)

• width_std (requires straightening)

• width_cv (requires straightening)

• width_skew (requires straightening)

• width_kurtosis (requires straightening)

• width_max (requires straightening)

• width_middle (requires straightening) : width in the middle (x-wise) of the mask

• bending_energy : quantification of the amount of energy required to bend the midline of the mask

Options¶

• morphology_computation_masks : The masks the features will be extracted from (e.g. ‘analysis/ch1_seg’ or ‘analysis/ch1_seg_str’)

• morphological_features : List of features to be extracted (e.g. [ ‘length’, ‘area’, ‘volume’, ‘width_mean’ ])

• pixelsize : physical size of a pixel in microns (e.g. 0.65)

Example¶

morphology_computation_masks: [ 'analysis/ch2_seg_str' ]
morphological_features: [ [ 'length', 'area', 'volume', 'width_mean' ] ]
pixelsize: [ 0.65 ]

This would compute the length, area, volume, and average width of all the straightened masks of the second channel. This would add 4 new columns to the analysis filemap :

• ch2_seg_str_length

• ch2_seg_str_area

• ch2_seg_str_volume

• ch2_seg_str_width_mean