Measure deproj

Measure deprojected cell shape

To measure cell properties with correction for the 2D projection artifacts, choose the Measures:Deprojected cells in the main pipeline interface.

This step allows you to measure morphological properties of cell, like their area, while correcting for their 3D->2D projection.

For bend tissue, projection from 3D to 2D and then measuring cell properties, as their area, on the 2D projection can generate small estimation error on the cell property (see deproj webpage).

If while doing the projection the mapping between the 3D and the 2D projection was saved, the height map, it is possible to get a better estimate of the cell 3D properties. Deproj is a matlab framework developed to estimate correct cell properties, see Herbert et al. 2021. Deprojpy is a python implementation of this tool. FishFeats relies on deprojpy to perform the deprojected calculation of cell properties.

For this, you have to precise the file that contains the z-map information (the real 3D position of each projected pixel). If you have done the projection with LocalZProjector or a similar tool, you can check options to also obtain this file along the projection results. If not, you can go to the step Cells:3D position in FishFeats and check the option Save Zmap. LocalZBackProj can also be used to estimate and build the z-map from the projection and the original 3D image.

Select the file that contains the z-map and click on Deproj to estimate the correct cell properties. A table with the measures will be displayed in the right side of the interface when the computation is done. See Deprojpy documentation for the description of the measures.

You can display the value of the deproj measure in each cell by selecting the corresponding feature in the Draw feature map option list.

To add these informations to the main FishFeatstable results that is saved in the results.csv file and reloaded everytime, press the button Add to results before to close this step. The added measures that comes from deprojected measurement are added with Deproj_ prefix to the name of the measure (e.g. Deproj_area). Hence, the measure of cell area ideally should be from the Deproj_area column that contains the corrected measure, while Area column would contains the purely 2D measure.