ERROR: MethodError: no method matching boundary_polygons_from_grid(::Matrix{UInt32}; grid_step::Float64) about baysor

[pakiessling]

@sarahyk Managed to get baysor 0.6.1 to work. The key is to downgrade Julia to 1.8.5 like so:

conda create -y -n baysor-test julia=1.8.5
conda activate baysor-test
julia -e 'using Pkg; Pkg.add(PackageSpec(url="https://github.com/kharchenkolab/Baysor.git")); Pkg.build()'

After that I tested baysor on the test osmfish data:

export JULIA_NUM_THREADS=30
baysor  run \
-c ./data/osmfish.toml -o ./output_osmfish3 -p --save-polygons=geojson ./data/mRNA_coords_raw_counting.csv :random

and received reports, the csv's and polygons 🥳

[pakiessling]

@VPetukhov

Can confirm that v0.6.1 and v.0.6.0 binaries produce the error on starmap example data when using prior segmentation.
Let me know if I can help somehow, would really love to use the package!

[sarahyk]

hi @pakiessling, have you had any success running the newer version of baysor through other installation methods like docker? I've been trying to find a solution to get this to run, but haven't had any luck yet

[pakiessling]

@sarahyk I did some more investigating and was able to avoid the boundary_polygons_from_grid error by removing the report flag from my command like this: baysor run -c ./data/starmap.toml -o ./output_dapi_star_nohup ./data/molecules.csv ./data/segmentation.tiff
The bad news is that no output at all is generated, just a log file with the last entry Processing complete...

This is also happening in the docker for me 😞

#78 mentions downgrading julia to 1.8.5 so I will give that a shot next...

[harrymueller]

Hi, I'm getting a similar issue with Baysor 0.6.1 and Julia 1.8.5 on Vizgen MERFISH data:
ERROR: LoadError: MethodError: no method matching boundary_polygons_from_grid(::Matrix{UInt32}; grid_step=5.0).

Command:
baysor+1.8.5 run ./transcript_subset_0.csv -o ./baysor-output -c ./baysor.toml --save-polygons GeoJSON --plot --count-matrix-format loom ./bin_mask.tiff

I've attached the stack trace, along with the configuration TOML:

• log.log
• baysor.toml

This only occurs when passing in the pre-segmented image, Baysor works fine without the image.

Additionally, the OSM-FISH example and the ISS example do not work - the same error occurs.

[HaojiaWu]

I am getting the same error. Have to go back to v0.5.1...
@VPetukhov can you take a look?

[VPetukhov]

Hi everyone,
Thanks for the report! Fixed that in the dev branch. Will release it with v0.6.2 soon.

[VPetukhov]

v0.6.2 is released now, so should be fixed