​​Problems encountered in boundary analysis​​

[Liaox-a]

Thank you for your wonderful tools!

When I used Spateo to identify the boundary lines between cell types, I found that when the boundary line identified by st.dd.identify_boundarywas discontinuous, st.dd.format_boundary_linecould not recognize the input pt_startand pt_end. The reason might be that ctrscontained multiple elements in this case. Although I could manually remove the discontinuous segments of the boundary line, I would still like to consult you on whether there is a better solution.

#user input
pt_start = (285,255)
pt_end = (259,280)
#digitize boundary related area
fmt_bdl_ls, fmt_bdl_img = st.dd.format_boundary_line(bdl_img, pt_start, pt_end)
st.dd.boundary_gridding(
adata=adata,
spatial_key="spatial",
boundary_line_img=fmt_bdl_img,
boundary_line_list=fmt_bdl_ls,
n_layer = 3,
layer_width=8,
init = True,
)

---

ValueError Traceback (most recent call last)
Cell In[232], line 6
3 pt_end = (259,280)
5 #digitize boundary related area
----> 6 fmt_bdl_ls, fmt_bdl_img = st.dd.format_boundary_line(bdl_img, pt_start, pt_end)
7 st.dd.boundary_gridding(
8 adata=adata,
9 spatial_key="spatial",
(...)
14 init = True,
15 )

File /share/appspace_data/shared_groups/BGI/USERS/liaox/.conda/envs/spateo/lib/python3.8/site-packages/spateo/digitization/utils_old.py:88, in format_boundary_line(boundary_line_img, pt_start, pt_end)
85 for pt in ctrs[0]: # should only contain a single contour
86 ctrs_pt_list.append((pt[0][0], pt[0][1]))
---> 88 start_idx = ctrs_pt_list.index(pt_start)
89 end_idx = ctrs_pt_list.index(pt_end)
90 formatted_bdl_list = ctrs_pt_list[min(start_idx, end_idx) : max(start_idx, end_idx) + 2]

ValueError: (285, 255) is not in list