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issue of reading visiumHD file #10
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I tried using |
Same issue on both Julia 1.8.4 and 1.7.3, any help for this?
Stacktrace: |
I am transitioning everything to Julia 1.10.4, as older versions have too many dependency issues. Could you please try this and let me know if you come across any problems? Thanks. |
Thanks for your reply, when running 'Pkg.add(url="https://github.com/TheHumphreysLab/CellScopes.jl")', I saw some issues: After cs.read_visiumHD(), the same error appeared again:
Stacktrace:
|
As mentioned in the link provided (https://github.com/HaojiaWu/CellScopes.jl/tree/dev), if you are using Julia v1.10.4, please use the following command to install: using Pkg
Pkg.add(PackageSpec(url="https://github.com/bicycle1885/Leiden.jl"))
Pkg.add(PackageSpec(url="https://github.com/HaojiaWu/CellScopes.jl", rev="dev")) I reinstalled it on a fresh Linux machine, and the methods described above worked for me when reading VisiumHD data. |
hd = cs.read_visiumHD(hd_dir)
Formatting cell polygons...
Progress: 100%[==================================================] Time: 0:00:5039m
Formatting cell polygons...
Progress: 100%[==================================================] Time: 0:00:02
Formatting cell polygons...
MethodError: no method matching Union{Matrix{ColorTypes.Gray{FixedPointNumbers.N0f8}}, Matrix{ColorTypes.RGB{FixedPointNumbers.N0f8}}, Matrix{ColorTypes.RGBA{FixedPointNumbers.N0f8}}}(::Matrix{ColorTypes.RGB{FixedPointNumbers.N0f16}})
Stacktrace:
[1] convert(#unused#::Type{Union{Matrix{ColorTypes.Gray{FixedPointNumbers.N0f8}}, Matrix{ColorTypes.RGB{FixedPointNumbers.N0f8}}, Matrix{ColorTypes.RGBA{FixedPointNumbers.N0f8}}}}, a::Matrix{ColorTypes.RGB{FixedPointNumbers.N0f16}})
@ Base ./array.jl:554
[2] convert(#unused#::Type{Union{Nothing, Matrix{ColorTypes.Gray{FixedPointNumbers.N0f8}}, Matrix{ColorTypes.RGB{FixedPointNumbers.N0f8}}, Matrix{ColorTypes.RGBA{FixedPointNumbers.N0f8}}}}, x::Matrix{ColorTypes.RGB{FixedPointNumbers.N0f16}})
@ Base ./some.jl:36
[3] CellScopes.VisiumImgObject(highresImage::Matrix{ColorTypes.RGB{FixedPointNumbers.N0f16}}, lowresImage::Matrix{ColorTypes.RGB{FixedPointNumbers.N0f16}}, fullresImage::Nothing, detectedTissue::Matrix{ColorTypes.RGB{FixedPointNumbers.N0f8}}, alignedImage::Matrix{ColorTypes.RGB{FixedPointNumbers.N0f8}}, jsonParameters::Dict{String, Any})
@ CellScopes ~/.julia/packages/CellScopes/pM38e/src/spatial/sp_objects.jl:249
[4] read_visiumHD(hd_dir::String; min_genes::Vector{Int64}, min_cells::Vector{Int64}, prefix::Nothing, postfix::Nothing, default_bin::String)
@ CellScopes ~/.julia/packages/CellScopes/pM38e/src/fileio.jl:660
[5] read_visiumHD(hd_dir::String)
@ CellScopes ~/.julia/packages/CellScopes/pM38e/src/fileio.jl:628
[6] top-level scope
@ In[6]:1
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