virtualembryo / foambryo Goto Github PK

Hi,
This is an amazing tool and thanks for making it available! Could you help me identify the problem with importing the some of the functions?

After using pip to install foambryo and foambryo[viewing], I am able to import and use the following:

1. from foambryo import plot_force_inference, plot_tension_inference
2. from foambryo import infer_forces

However, the following imports do not work and I get a similar error for each one:

Error: ImportError: cannot import name 'dcel_mesh_from_segmentation_mask' from 'foambryo' (C:\ProgramData\anaconda3\Lib\site-packages\foambryo_init_.py)

Functions that cause the error above:

1. from foambryo import dcel_mesh_from_segmentation_mask
2. from foambryo.viewing import plot_force_inference, plot_tension_inference
3. from foambryo import infer_pressures, infer_tensions
4. from foambryo import PressureComputationMethod, TensionComputationMethod

Since the dcel_mesh_from_segmentation_mask cannot be imported, I am using the following method to build the mesh from the segmentation mask and use plot_force_interface:

Load the labels

import skimage.io as io
Segmentation = io.imread('E:/ablation/ABTZL-cftr-hsp-h2a-tdtom-col8a1a-gfpCaax-2dpf/fish1/T_-1/closed_stack.tif')

Reconstruct a multimaterial mesh from the labels

DW = geometry_reconstruction_3d(Segmentation,min_dist = 3)
Verts, Faces_multimaterial = DW.return_mesh()
Mesh = DCEL_Data(Verts,Faces_multimaterial)

Hi all,

Thank you for this awesome package - very exciting!
I just had a question about the scaling of the image after import. I'm trying to use this on confocal data that's not isotropic, but I noticed my image was scaled isotopically after importing and running the viewer so it looked a bit squashed. I can overcome this by rescaling z manually before feeding it into the package pipeline. However, I was just wondering if there was anyway to set the x,y,z resolution from the metadata before generating the mesh as I assume it would change any tension/pressure inferences not having the correct shape?

Thank you for any help,

Zimeng