Parameters settings

The PyStack3D workflow parameters are defined in a params.toml file that is structured as follows:

• The first parameters are related to the general parameters that specify the conditions of the workflow execution.

• The following ‘encapsulated’ parameters are related to the conditions of each process step execution.

To illustrate each of the process step we will consider hereafter the synthetic test case obtained by adding defects to an original stack (which is named ‘target’ in what follows) composed of 300 x 300 x 300 voxels. The defects to be removed corresponds to:

• curtaining effects in some slices

• a background effect (defined from a polynom x*y*z),

• shifts along the x-axis (for slices in [20-70])

• changes in brightness (for slices in [70-100])

• a non-uniform sampling (inter-slice distance dz changing from 0.01 to 0.02 at slice 100)

Illustration of the synthetic use case: 3D visualisations and cut-planes corresponding to Z=83 and Y=150.

• General Parameters
• Cropping
• Background removal
• Intensity rescaling
• Registration
• Destriping
• Resampling
• Cropping final