This flash workshop is the 2nd of 6 different others, presenting 6 different applications of free (Fiji) and commercial 3D software (Imaris) from visualization to data analysis. The advent of machine learning has profoundly changed classical thresholding and object classification methods. It is now possible to "teach" the software what our structures of interest look like. It is indeed sometimes complex to discriminate in 3D our structures of interest just from intensity or shape. Object detection by machine learning allows to "contextualize" with more parameters and power the information of our structures. Software for Pixel classification in 3D by machine learning are still rare today, but it tends to develop strongly.