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Re: error with opening a ome.tiff file. #106

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mdhe1248 opened this issue Sep 1, 2023 · 8 comments
Open

Re: error with opening a ome.tiff file. #106

mdhe1248 opened this issue Sep 1, 2023 · 8 comments
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@mdhe1248
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mdhe1248 commented Sep 1, 2023

Hi,

My images was acquired by a Zeiss confocal microscope and saved images as ome.tiff. When I tried to load the file in julia, I got this error:

julia> load(movingfns[10])                                                                                                                                                             
Error encountered while load FileIO.File{FileIO.DataFormat{:OMETIFF}, String}("/media/donghoon_001/imaging_dat/birc_nikon_confocal/230808_and_230725_adlib_fasted_refed/tif/230725_2_3_
3_2_refed_round3_dapi_hcrt_gal_cartpt_Stitch.ome.tiff").                                                                                                                               
                                                                                                                                                                                       
Fatal error:                                                                                                                                                                           
ERROR: ArgumentError: collection must be non-empty 
Stacktrace:                                                                                                                                                                  [194/1469]
  [1] first                                                                                                                                                                            
    @ ./abstractarray.jl:466 [inlined]                                                                                                                                                 
  [2] inmemoryarray(ifds::OrderedCollections.OrderedDict{NTuple{4, Int64}, Tuple{TiffImages.TiffFile{UInt32}, TiffImages.IFD{UInt32}}}, dims::NamedTuple{(:Y, :X, :Z, :C, :T, :P), NTup
le{6, Int64}}; verbose::Bool)                                                                                                                                                          
    @ OMETIFF ~/.julia/packages/OMETIFF/3RcZb/src/loader.jl:122                                                                                                                        
  [3] load(io::FileIO.Stream{FileIO.DataFormat{:OMETIFF}, IOStream, String}; dropunused::Bool, verbose::Bool, inmemory::Bool)                                                          
    @ OMETIFF ~/.julia/packages/OMETIFF/3RcZb/src/loader.jl:90
  [4] load                                   
    @ ~/.julia/packages/OMETIFF/3RcZb/src/loader.jl:29 [inlined]
  [5] #33                                    
    @ ~/.julia/packages/OMETIFF/3RcZb/src/loader.jl:3 [inlined]
  [6] open(f::OMETIFF.var"#33#34"{Bool, Bool}, args::FileIO.File{FileIO.DataFormat{:OMETIFF}, String}; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ Base ./io.jl:395                       
  [7] open                                   
    @ ./io.jl:392 [inlined]                  
  [8] #load#32                               
    @ ~/.julia/packages/OMETIFF/3RcZb/src/loader.jl:2 [inlined]
  [9] load(f::FileIO.File{FileIO.DataFormat{:OMETIFF}, String})
    @ OMETIFF ~/.julia/packages/OMETIFF/3RcZb/src/loader.jl:1
 [10] #invokelatest#2
    @ ./essentials.jl:819 [inlined]                                                                                                                                          [173/1469]
 [11] invokelatest                           
    @ ./essentials.jl:816 [inlined]          
 [12] action(::Symbol, ::Vector{Union{Base.PkgId, Module}}, ::FileIO.Formatted; options::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ FileIO ~/.julia/packages/FileIO/BE7iZ/src/loadsave.jl:219
 [13] action                                 
    @ ~/.julia/packages/FileIO/BE7iZ/src/loadsave.jl:196 [inlined]
 [14] action(::Symbol, ::Vector{Union{Base.PkgId, Module}}, ::Symbol, ::String; options::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ FileIO ~/.julia/packages/FileIO/BE7iZ/src/loadsave.jl:185
 [15] action                                 
    @ ~/.julia/packages/FileIO/BE7iZ/src/loadsave.jl:185 [inlined]
 [16] load(::String; options::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ FileIO ~/.julia/packages/FileIO/BE7iZ/src/loadsave.jl:113
 [17] load(::String)                         
    @ FileIO ~/.julia/packages/FileIO/BE7iZ/src/loadsave.jl:109
 [18] top-level scope                        
    @ REPL[266]:1                            
Stacktrace:                                  
 [1] handle_error(e::ArgumentError, q::Base.PkgId, bt::Vector{Union{Ptr{Nothing}, Base.InterpreterIP}})
   @ FileIO ~/.julia/packages/FileIO/BE7iZ/src/error_handling.jl:61
 [2] handle_exceptions(exceptions::Vector{Tuple{Any, Union{Base.PkgId, Module}, Vector}}, action::String)
   @ FileIO ~/.julia/packages/FileIO/BE7iZ/src/error_handling.jl:56                                                                                                          [152/1469]
 [3] action(::Symbol, ::Vector{Union{Base.PkgId, Module}}, ::FileIO.Formatted; options::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
   @ FileIO ~/.julia/packages/FileIO/BE7iZ/src/loadsave.jl:228
 [4] action                                  
   @ ~/.julia/packages/FileIO/BE7iZ/src/loadsave.jl:196 [inlined]
 [5] action(::Symbol, ::Vector{Union{Base.PkgId, Module}}, ::Symbol, ::String; options::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
   @ FileIO ~/.julia/packages/FileIO/BE7iZ/src/loadsave.jl:185
 [6] action                                  
   @ ~/.julia/packages/FileIO/BE7iZ/src/loadsave.jl:185 [inlined]
 [7] load(::String; options::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
   @ FileIO ~/.julia/packages/FileIO/BE7iZ/src/loadsave.jl:113
 [8] load(::String)                          
   @ FileIO ~/.julia/packages/FileIO/BE7iZ/src/loadsave.jl:109
 [9] top-level scope                         
   @ REPL[266]:1

Interestingly, I was able to load the same files in Fiji (but the pixel parameters were were not correct). I also checked the header file with tiffcomment command:

<?xml version="1.0" encoding="UTF-8" standalone="yes" ?>
<!--Warning: this comment is an OME-XML metadata block, which contains crucial dimensional parameters and other important metadata. Please edit cautiously (if at all), and back up the original data before doing so. For more information, see the OME-TIFF web site: http://loci.wisc.edu/ome/ome-tiff.html.-->
<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2010-04" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2010-04/ome.xsd http://www.openmicroscopy.org/Schemas/OME/2010-04/ome.xsd">
  <Instrument ID="Instrument:0">
    <Detector Gain="1" Voltage="650" Zoom="1" AmplificationGain="1" ID="Detector:0:0" Type="PMT" />
    <Detector Gain="1" Voltage="650" Zoom="1" AmplificationGain="1" ID="Detector:1:0" Type="PMT" />
    <Detector Gain="1" Voltage="650" Zoom="1" AmplificationGain="1" ID="Detector:1:1" Type="PMT" />
    <Detector Gain="1" Voltage="649.981" Zoom="1" AmplificationGain="1" ID="Detector:2:0" Type="PMT" />
    <Objective ID="Objective:0" Immersion="Air" LensNA="0.45" NominalMagnification="10" />
  </Instrument>
  <Image ID="Image:1" Name="230725_2_3_2_6_fasted_round3_dapi_hcrt_gal_cartpt_Stitch.ome">
    <AcquiredDate>2023-08-30T00:43:52</AcquiredDate>
    <Description></Description>
    <InstrumentRef ID="Instrument:0" />
    <ObjectiveSettings ID="Objective:0" />
    <Pixels ID="Pixels:Uint12" DimensionOrder="XYZCT" Type="uint12" SizeX="2867" SizeY="4712" SizeZ="5" SizeT="1" SizeC="4" PhysicalSizeX="0.830266" PhysicalSizeY="0.830266" PhysicalSizeZ="6">
      <Channel ID="Channel:0" Name="Ch1-T1" PinholeSize="25.835" Fluor="DAPI" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:0:0" Binning="1x1" />
      </Channel>
      <Channel ID="Channel:1" Name="Ch1-T2" PinholeSize="28.9734" Fluor="Alexa Fluor 488" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:1:0" Binning="1x1" />
      </Channel>
      <Channel ID="Channel:2" Name="Ch2 GaAsP-T2" PinholeSize="28.9734" Fluor="Alexa Fluor 647" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:1:1" Binning="1x1" />
      </Channel>
      <Channel ID="Channel:3" Name="Ch2 GaAsP-T3" PinholeSize="33.3092" Fluor="Alexa Fluor 546" SamplesPerPixel="1">
        <DetectorSettings ID="Detector:2:0" Binning="1x1" />
      </Channel>
      <TiffData />
      <Plane TheZ="0" TheT="0" TheC="0" DeltaT="0" PositionX="0" PositionY="0" PositionZ="0" />
      <Plane TheZ="0" TheT="0" TheC="1" DeltaT="0" PositionX="0" PositionY="0" PositionZ="0" />
      <Plane TheZ="0" TheT="0" TheC="2" DeltaT="0" PositionX="0" PositionY="0" PositionZ="0" />
      <Plane TheZ="0" TheT="0" TheC="3" DeltaT="0" PositionX="0" PositionY="0" PositionZ="0" />
      <Plane TheZ="1" TheT="0" TheC="0" DeltaT="0" PositionX="0" PositionY="0" PositionZ="0" />
      <Plane TheZ="1" TheT="0" TheC="1" DeltaT="0" PositionX="0" PositionY="0" PositionZ="0" />
      <Plane TheZ="1" TheT="0" TheC="2" DeltaT="0" PositionX="0" PositionY="0" PositionZ="0" />
      <Plane TheZ="1" TheT="0" TheC="3" DeltaT="0" PositionX="0" PositionY="0" PositionZ="0" />
      <Plane TheZ="2" TheT="0" TheC="0" DeltaT="0" PositionX="0" PositionY="0" PositionZ="0" />
      <Plane TheZ="2" TheT="0" TheC="1" DeltaT="0" PositionX="0" PositionY="0" PositionZ="0" />
      <Plane TheZ="2" TheT="0" TheC="2" DeltaT="0" PositionX="0" PositionY="0" PositionZ="0" />
      <Plane TheZ="2" TheT="0" TheC="3" DeltaT="0" PositionX="0" PositionY="0" PositionZ="0" />
      <Plane TheZ="3" TheT="0" TheC="0" DeltaT="0" PositionX="0" PositionY="0" PositionZ="0" />
      <Plane TheZ="3" TheT="0" TheC="1" DeltaT="0" PositionX="0" PositionY="0" PositionZ="0" />
      <Plane TheZ="3" TheT="0" TheC="2" DeltaT="0" PositionX="0" PositionY="0" PositionZ="0" />
      <Plane TheZ="3" TheT="0" TheC="3" DeltaT="0" PositionX="0" PositionY="0" PositionZ="0" />
      <Plane TheZ="4" TheT="0" TheC="0" DeltaT="0" PositionX="0" PositionY="0" PositionZ="0" />
      <Plane TheZ="4" TheT="0" TheC="1" DeltaT="0" PositionX="0" PositionY="0" PositionZ="0" />
      <Plane TheZ="4" TheT="0" TheC="2" DeltaT="0" PositionX="0" PositionY="0" PositionZ="0" />
      <Plane TheZ="4" TheT="0" TheC="3" DeltaT="0" PositionX="0" PositionY="0" PositionZ="0" />
    </Pixels>
  </Image>
</OME>

Also I have the "original" czi file format. If I open it in fiji and store it as ome.tif, Julia could load the resulting ome.tif file. While I can convert all files in Fiji, I wanted to check if these is better ways to solve this issue.
@mdhe1248
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mdhe1248 commented Sep 1, 2023

TiffImages.jl package opened the file without an error, although the axis information is missing.

@tlnagy
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tlnagy commented Sep 19, 2023

OMETIFF uses TiffImages.jl as its engine so it must be an OMEXML-related issue. Do you mind sharing a minimal image that can reproduce this? You can either upload here or email it to the email address on my profile.

@mdhe1248
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I will come back with a sample image in a few days...

@tlnagy
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tlnagy commented Mar 21, 2024

Bump. Are you still running into this issue?

@mdhe1248
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Oh, Sorry.
I have been preoccupied with other stuff.
I will close it for now and open it with an example image if I encounter this issue again.

@mastrof
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mastrof commented Apr 19, 2024 •
edited
Loading

I have also been working on a Zeiss setup recently and can't open the files. If I first open them in FIJI and export them to OME-TIFF then they seem to work. I cannot access this system anymore so I can't get lightweight images to reproduce the error, but I'm willing to share one of the stacks I have (~5 GB) if it helps to identify the issue.

EDIT: Whether they open or not after the FIJI export seems to be random, but the error is different. E.g., if I open it, slice it down (in this case taking only 5 frames) and export it, then I get indexing issues:

Fatal error:                                                                                                                                                                                                        
ERROR: BoundsError: attempt to access 5-element Vector{Unitful.Quantity{Float64, 𝐓, Unitful.FreeUnits{(s,), 𝐓, nothing}}} at index [6]                                                                              
Stacktrace:                                                                                                                                                                                                         
  [1] setindex!(A::Vector{Unitful.Quantity{…}}, x::Unitful.Quantity{Float64, 𝐓, Unitful.FreeUnits{…}}, i1::Int64)                                                                                                   
    @ Base ./array.jl:1021                                                                                                                                                                                          
  [2] get_elapsed_times(containers::Vector{…}, master_dims::@NamedTuple{…}, masteraxis::Vector{…}; default_unit::Unitful.FreeUnits{…})
    @ OMETIFF ~/.julia/packages/OMETIFF/Jsw4Z/src/parsing.jl:235                                          
  [3] get_elapsed_times(containers::Vector{…}, master_dims::@NamedTuple{…}, masteraxis::Vector{…})        
    @ OMETIFF ~/.julia/packages/OMETIFF/Jsw4Z/src/parsing.jl:202                                          
  [4] load(io::Stream{DataFormat{:OMETIFF}, IOStream, String}; dropunused::Bool, verbose::Bool, inmemory::Bool)
    @ OMETIFF ~/.julia/packages/OMETIFF/Jsw4Z/src/loader.jl:87                                            
  [5] load                                           
    @ ~/.julia/packages/OMETIFF/Jsw4Z/src/loader.jl:29 [inlined]                                          
  [6] #33                                            
    @ ~/.julia/packages/OMETIFF/Jsw4Z/src/loader.jl:3 [inlined]                                           
  [7] open(f::OMETIFF.var"#33#34"{Bool, Bool}, args::File{DataFormat{:OMETIFF}, String}; kwargs::@Kwargs{})
    @ Base ./io.jl:396                               
  [8] open                                           
    @ Base ./io.jl:393 [inlined]                     
  [9] #load#32                                       
    @ OMETIFF ~/.julia/packages/OMETIFF/Jsw4Z/src/loader.jl:2 [inlined]                                   
 [10] load(f::File{DataFormat{:OMETIFF}, String})    
    @ OMETIFF ~/.julia/packages/OMETIFF/Jsw4Z/src/loader.jl:1                                             
 [11] #invokelatest#2                                
    @ ./essentials.jl:887 [inlined]                  
 [12] invokelatest                                   
    @ ./essentials.jl:884 [inlined]                  
 [13] action(::Symbol, ::Vector{Union{Base.PkgId, Module}}, ::Formatted; options::@Kwargs{})              
    @ FileIO ~/.julia/packages/FileIO/xOKyx/src/loadsave.jl:219                                           
 [14] action                                         
    @ ~/.julia/packages/FileIO/xOKyx/src/loadsave.jl:196 [inlined]                                        
 [15] action                                         
    @ ~/.julia/packages/FileIO/xOKyx/src/loadsave.jl:185 [inlined]                                        
 [16] load(::String; options::@Kwargs{})             
    @ FileIO ~/.julia/packages/FileIO/xOKyx/src/loadsave.jl:113                                           
 [17] load(::String)                                 
    @ FileIO ~/.julia/packages/FileIO/xOKyx/src/loadsave.jl:109                                           
 [18] top-level scope                                
    @ REPL[41]:1                                     
Stacktrace:
 [1] handle_error(e::BoundsError, q::Base.PkgId, bt::Vector{Union{Ptr{Nothing}, Base.InterpreterIP}})
   @ FileIO ~/.julia/packages/FileIO/xOKyx/src/error_handling.jl:61
 [2] handle_exceptions(exceptions::Vector{Tuple{Any, Union{Base.PkgId, Module}, Vector}}, action::String)
   @ FileIO ~/.julia/packages/FileIO/xOKyx/src/error_handling.jl:56
 [3] action(::Symbol, ::Vector{Union{Base.PkgId, Module}}, ::Formatted; options::@Kwargs{})
   @ FileIO ~/.julia/packages/FileIO/xOKyx/src/loadsave.jl:228
 [4] action
   @ ~/.julia/packages/FileIO/xOKyx/src/loadsave.jl:196 [inlined]
 [5] action
   @ ~/.julia/packages/FileIO/xOKyx/src/loadsave.jl:185 [inlined]
 [6] load(::String; options::@Kwargs{})
   @ FileIO ~/.julia/packages/FileIO/xOKyx/src/loadsave.jl:113
 [7] load(::String)
   @ FileIO ~/.julia/packages/FileIO/xOKyx/src/loadsave.jl:109
 [8] top-level scope
   @ REPL[41]:1

@tlnagy tlnagy reopened this Apr 22, 2024
@neelakss
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I am having the same issue loading the tiff files.

Error encountered while load FileIO.File{FileIO.DataFormat{:OMETIFF}, String}("morphology_mip.ome.tif").

Fatal error:
ERROR: LoadError: ArgumentError: collection must be non-empty
Stacktrace:
[1] first
@ ./abstractarray.jl:473 [inlined]
[2] inmemoryarray(ifds::OrderedCollections.OrderedDict{NTuple{4, Int64}, Tuple{TiffImages.TiffFile{UInt64}, TiffImages.IFD{UInt64}}}, dims::@NamedTuple{Y::Int64, X::Int64, Z::Int64, C::Int64, T::Int64, P::Int64}; verbose::Bool)
@ OMETIFF ~/.julia/packages/OMETIFF/Jsw4Z/src/loader.jl:122
[3] load(io::FileIO.Stream{FileIO.DataFormat{:OMETIFF}, IOStream, String}; dropunused::Bool, verbose::Bool, inmemory::Bool)
@ OMETIFF ~/.julia/packages/OMETIFF/Jsw4Z/src/loader.jl:90
[4] load
@ ~/.julia/packages/OMETIFF/Jsw4Z/src/loader.jl:29 [inlined]
[5] #33
@ ~/.julia/packages/OMETIFF/Jsw4Z/src/loader.jl:3 [inlined]
[6] open(f::OMETIFF.var"#33#34"{Bool, Bool}, args::FileIO.File{FileIO.DataFormat{:OMETIFF}, String}; kwargs::@kwargs{})
@ Base ./io.jl:396
[7] open
@ ./io.jl:393 [inlined]
[8] #load#32
@ ~/.julia/packages/OMETIFF/Jsw4Z/src/loader.jl:2 [inlined]
[9] load(f::FileIO.File{FileIO.DataFormat{:OMETIFF}, String})
@ OMETIFF ~/.julia/packages/OMETIFF/Jsw4Z/src/loader.jl:1
[10] #invokelatest#2
@ ./essentials.jl:892 [inlined]
[11] invokelatest
@ ./essentials.jl:889 [inlined]
[12] action(::Symbol, ::Vector{Union{Base.PkgId, Module}}, ::FileIO.Formatted; options::@kwargs{})
@ FileIO ~/.julia/packages/FileIO/xOKyx/src/loadsave.jl:219
[13] action
@ ~/.julia/packages/FileIO/xOKyx/src/loadsave.jl:196 [inlined]
[14] action
@ ~/.julia/packages/FileIO/xOKyx/src/loadsave.jl:185 [inlined]
[15] load(::String; options::@kwargs{})
@ FileIO ~/.julia/packages/FileIO/xOKyx/src/loadsave.jl:113
[16] load
@ ~/.julia/packages/FileIO/xOKyx/src/loadsave.jl:109 [inlined]
[17] load_segmentation_mask(path::String)
@ Baysor.DataLoading ~/.julia/packages/Baysor/6dGr2/src/data_loading/prior_segmentation.jl:60
[18] load_prior_segmentation(file::String, pos_data::Matrix{Float64}; min_molecules_per_segment::Int64)
@ Baysor.DataLoading ~/.julia/packages/Baysor/6dGr2/src/data_loading/cli_wrappers.jl:30
[19] load_prior_segmentation
@ ~/.julia/packages/Baysor/6dGr2/src/data_loading/cli_wrappers.jl:27 [inlined]
[20] load_prior_segmentation!(path::String, df_spatial::DataFrames.DataFrame, pos_data::Matrix{Float64}; min_molecules_per_segment::Int64, min_mols_per_cell::Int64)
@ Baysor.DataLoading ~/.julia/packages/Baysor/6dGr2/src/data_loading/cli_wrappers.jl:218
[21] load_prior_segmentation!(df_spatial::DataFrames.DataFrame, prior_segmentation::String, opts::Baysor.Utils.SegmentationOptions; min_molecules_per_cell::Int64, min_molecules_per_segment::Int64, plot::Bool)
@ Baysor.CommandLine ~/.julia/packages/Baysor/6dGr2/src/cli/main.jl:197
[22] run(coordinates::String, prior_segmentation::String; config::Baysor.Utils.RunOptions, x_column::String, y_column::String, z_column::String, gene_column::String, min_molecules_per_cell::Int64, scale::Float64, scale_std::String, n_clusters::Int64, prior_segmentation_confidence::Float64, output::String, plot::Bool, save_polygons::String, no_ncv_estimation::Bool, count_matrix_format::String)
@ Baysor.CommandLine ~/.julia/packages/Baysor/6dGr2/src/cli/main.jl:108
[23] command_main(ARGS::Vector{String})
@ Baysor.CommandLine ~/.julia/packages/Comonicon/F3QqZ/src/codegen/julia.jl:343
[24] command_main()
@ Baysor.CommandLine ~/.julia/packages/Comonicon/F3QqZ/src/codegen/julia.jl:90
[25] command_main(; kwargs::@kwargs{})
@ Baysor ~/.julia/packages/Baysor/6dGr2/src/Baysor.jl:41
[26] top-level scope
@ ~/.julia/bin/baysor:15
Stacktrace:
[1] handle_error(e::ArgumentError, q::Base.PkgId, bt::Vector{Union{Ptr{Nothing}, Base.InterpreterIP}})
@ FileIO ~/.julia/packages/FileIO/xOKyx/src/error_handling.jl:61
[2] handle_exceptions(exceptions::Vector{Tuple{Any, Union{Base.PkgId, Module}, Vector}}, action::String)
@ FileIO ~/.julia/packages/FileIO/xOKyx/src/error_handling.jl:56
[3] action(::Symbol, ::Vector{Union{Base.PkgId, Module}}, ::FileIO.Formatted; options::@kwargs{})
@ FileIO ~/.julia/packages/FileIO/xOKyx/src/loadsave.jl:228
[4] action
@ ~/.julia/packages/FileIO/xOKyx/src/loadsave.jl:196 [inlined]
[5] action
@ ~/.julia/packages/FileIO/xOKyx/src/loadsave.jl:185 [inlined]
[6] load(::String; options::@kwargs{})
@ FileIO ~/.julia/packages/FileIO/xOKyx/src/loadsave.jl:113
[7] load
@ ~/.julia/packages/FileIO/xOKyx/src/loadsave.jl:109 [inlined]
[8] load_segmentation_mask(path::String)
@ Baysor.DataLoading ~/.julia/packages/Baysor/6dGr2/src/data_loading/prior_segmentation.jl:60
[9] load_prior_segmentation(file::String, pos_data::Matrix{Float64}; min_molecules_per_segment::Int64)
@ Baysor.DataLoading ~/.julia/packages/Baysor/6dGr2/src/data_loading/cli_wrappers.jl:30
[10] load_prior_segmentation
@ ~/.julia/packages/Baysor/6dGr2/src/data_loading/cli_wrappers.jl:27 [inlined]
[11] load_prior_segmentation!(path::String, df_spatial::DataFrames.DataFrame, pos_data::Matrix{Float64}; min_molecules_per_segment::Int64, min_mols_per_cell::Int64)
@ Baysor.DataLoading ~/.julia/packages/Baysor/6dGr2/src/data_loading/cli_wrappers.jl:218
[12] load_prior_segmentation!(df_spatial::DataFrames.DataFrame, prior_segmentation::String, opts::Baysor.Utils.SegmentationOptions; min_molecules_per_cell::Int64, min_molecules_per_segment::Int64, plot::Bool)
@ Baysor.CommandLine ~/.julia/packages/Baysor/6dGr2/src/cli/main.jl:197
[13] run(coordinates::String, prior_segmentation::String; config::Baysor.Utils.RunOptions, x_column::String, y_column::String, z_column::String, gene_column::String, min_molecules_per_cell::Int64, scale::Float64, scale_std::String, n_clusters::Int64, prior_segmentation_confidence::Float64, output::String, plot::Bool, save_polygons::String, no_ncv_estimation::Bool, count_matrix_format::String)
@ Baysor.CommandLine ~/.julia/packages/Baysor/6dGr2/src/cli/main.jl:108
[14] command_main(ARGS::Vector{String})
@ Baysor.CommandLine ~/.julia/packages/Comonicon/F3QqZ/src/codegen/julia.jl:343
[15] command_main()
@ Baysor.CommandLine ~/.julia/packages/Comonicon/F3QqZ/src/codegen/julia.jl:90
[16] command_main(; kwargs::@kwargs{})
@ Baysor ~/.julia/packages/Baysor/6dGr2/src/Baysor.jl:41
[17] top-level scope
@ ~/.julia/bin/baysor:15
in expression starting at /home/nsoni/.julia/bin/baysor:15

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tlnagy commented May 20, 2024

Unfortunately, the error messages aren't super helpful here. Does anyone have a small-ish file (<100 MB) that reproduces this error that they can share with me?

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