Quantification on 20X images ?

[drupani]

Hello,
BigFish is a great tool, thank you for the notebooks, they are extremely helpful!!

I am trying to run the quantification on 20X images, is the tool capable of running on it ?

IndexError Traceback (most recent call last)
Cell In[6], line 1
----> 1 fov_results = multistack.extract_cell(
2 cell_label=cell_label,
3 ndim=3,
4 nuc_label=nuc_label,
5 rna_coord=spots,
6 others_image={"dapi": nuc, "smfish": rna})
7 print("number of cells identified: {0}".format(len(fov_results)))
8 print (fov_results)

File ~/miniconda3/lib/python3.11/site-packages/bigfish/multistack/postprocess.py:441, in extract_cell(cell_label, ndim, nuc_label, rna_coord, others_coord, image, others_image, remove_cropped_cell, check_nuc_in_cell)
438 continue
440 # get boundaries coordinates for nucleus
--> 441 nuc_coord = from_binary_to_coord(nuc_mask)
442 nuc_coord = complete_coord_boundaries(nuc_coord)
443 nuc_coord[:, 0] -= min_y

File ~/miniconda3/lib/python3.11/site-packages/bigfish/multistack/postprocess.py:953, in from_binary_to_coord(binary)
950 binary_ = np.pad(binary, [(1, 1)], mode="constant")
952 # get external boundaries coordinates
--> 953 coord = find_contours(binary_, level=0)[0].astype(dtype)
955 # remove the pad
956 coord -= 1

IndexError: list index out of range

This is the error I am getting.
Thank you