Paper review

[danasolav]

Hello @gianthk I have a few comments/suggestions about the current version of the paper:

• [X] Line 20: is the package limited to isotropic linear elasticity? If not, please describe what other material models are available.

  indeed, 'Linear elastic' in this sentence is ambiguous since it refers only to the first cited study. We have removed 'Linear elastic' leaving the introduction sentence more general. In the examples section (line XX) we have mentioned that the package can be also used for non-linear plastic simulations.

• [X] Lines 32-54 describing the pipeline elements: the first two (image preprocessing and meshing) is in the same paragraph and the third is in a new paragraph. Please make it consistent. Also, please add a description for FE model solution and results postprocessing as well.

• [X] Line 35: what is Otsu's method? I don't see it mentioned in the reference (Walt 2014).

  ref to the method for automatic image thresholding (Otsu 1979) added. Walt 2014 is the ref to scikit-image where an algorithm for Otsu's thresholding method is contained.

• [X] Line 36: should be "clusters of voxels"

• [X] Please add the references related to the LHDL project as regular references in the list, and not only as links.

• [X] Line 71: The word "Project" after (LHDL) can be deleted.

• [X] Kine 73: should be "a partner of this project".

• [X] Line 74: the hyphen in linear-elastic can be removed.

• [ ] Line 75: what about the Poisson ratio? can it also be calculated?

• [X] What other examples are included besides the described main application?

  we have modified the last sentence of the examples section: "Ciclope can be applied to microCT scans other than trabecular bone and in fields other than biomechanics. A simulation of a mechanical test of a whole human teeth, and a non-linear analysis of metal foam plasticity are illustrated in the software examples."

• [X] Please check all the cited software, packages, and repositories if they have citable publications other than the web address.

[gianthk]

* [ ]  Line 75: what about the Poisson ratio? can it also be calculated?

In principle yes. The tissue poisson ratio can be calculated using the Virtual Fields Method (VFM), as illustrated in a work by Gillard et. al. 2014. This work used Digital Volume Correlation to measure local strain fields. There seem to be no report of the VFM applied to microFE simulations. The apparent level poisson ration of trabecular bone could be calculated (in a less complicated way) from displacements perpendicular to the load direction. However, the reason why microFE is more often applied to estimate the elastic modulus is that apparent level FE estimates can be combined with mechanical tests of the effective apparent modulus. Under the assumption of linear elasticity this allows to infer the tissue level elastic modulus of trabecular tissue. This is not the case for the poisson's ratio. We believe that this discussion on the possible uses of microFE simulations and mechanical testing exceeds the scope of our report of a python package for the generation of FE models from microCT images.

[gianthk]

chek all the cited software, packages, and repositories if they have citable publications other than the web address.

all checked. tha sw/packages ticked in the list below include citing instructions which we have followed. for the remaining 4 we used the web page.

• [X] scikit-image
• [X] scipy
• [X] paraview
• [X] calculix
• [ ] abaqus
• [X] meshio
• [X] cgal
• [X] pygalmesh
• [X] pymcubes
• [ ] itkwidgets
• [ ] ccx2paraview

[gianthk]

@danasolav please check the latest version of the paper vs your list of comments/issues above. if you agree with all our replies please close this issue