save_segmentation_results failing for some FOVs

[sam-mick]

Hi there,

I'm running Baysor on CosMx data, using Mesmer segmentation as a prior.

Some FOVs are failing to get saved after segmentation with Baysor, but the error only seems to occur in the actual saving step.

#150 (comment) had the same error, but the issue isn't just with transcripts at -1 - it can occur at any value.

Here's an example, if the transcript file (tx in CosMx) has very few transcripts at a Z value of -1, then it will fail.

# A tibble: 9 × 2
      z count
  <int> <int>
1    -1     1
2     0   440
3     1  1149
4     2  1188
5     3   977
6     4   867
7     5   742
8     6   602
9     7   520

Likewise for transcripts at a Z value of 8:

# A tibble: 9 × 2
      z count
  <int> <int>
1     0   920
2     1  2274
3     2  2579
4     3  2270
5     4  2061
6     5  2104
7     6  1912
8     7  1906
9     8     2

And here's the output of running Baysor:

baysor/bin/baysor run temp_tx_file.csv FOV_1_mesmer_mask.tif -c baysor/cosmx.toml --count-matrix-format 'tsv'

[12:14:03] Info: Run R97afc05f1
[12:14:03] Info: (2025-12-04) Run Baysor v0.7.1
[12:14:03] Info: Loading data...
[12:14:06] Info: Excluding genes: Negative1, Negative10, Negative3, Negative4, Negative5, Negative6, Negative7, Negative8, Negative9, SystemControl10, SystemControl100, SystemControl101, SystemControl104, SystemControl111, SystemControl113, SystemControl118, SystemControl121, SystemControl126, SystemControl127, SystemControl128, SystemControl129, SystemControl130, SystemControl131, SystemControl132, SystemControl133, SystemControl136, SystemControl138, SystemControl139, SystemControl14, SystemControl141, SystemControl142, SystemControl144, SystemControl145, SystemControl146, SystemControl148, SystemControl149, SystemControl15, SystemControl150, SystemControl151, SystemControl152, SystemControl155, SystemControl159, SystemControl16, SystemControl160, SystemControl161, SystemControl164, SystemControl168, SystemControl169, SystemControl17, SystemControl171, SystemControl172, SystemControl174, SystemControl177, SystemControl18, SystemControl180, SystemControl182, SystemControl183, SystemControl184, SystemControl185, SystemControl187, SystemControl188, SystemControl190, SystemControl193, SystemControl197, SystemControl2, SystemControl21, SystemControl22, SystemControl23, SystemControl24, SystemControl26, SystemControl27, SystemControl3, SystemControl30, SystemControl34, SystemControl4, SystemControl43, SystemControl47, SystemControl48, SystemControl5, SystemControl50, SystemControl51, SystemControl52, SystemControl54, SystemControl55, SystemControl57, SystemControl58, SystemControl59, SystemControl61, SystemControl62, SystemControl65, SystemControl66, SystemControl67, SystemControl7, SystemControl71, SystemControl72, SystemControl73, SystemControl74, SystemControl75, SystemControl78, SystemControl8, SystemControl80, SystemControl81, SystemControl85, SystemControl86, SystemControl89, SystemControl9, SystemControl90, SystemControl94, SystemControl95, SystemControl96, SystemControl97
[12:14:06] Info: Loaded 48992 transcripts, 991 genes.
[12:14:06] Info: Loading segmentation mask...
[12:14:08] Warning: Minimum transcript coordinates are < 1: (1, 0). Filling it with 0.
└ Baysor.DataLoading /home/viktor_petukhov/.julia/dev/Baysor/src/data_loading/prior_segmentation.jl:30
[12:14:08] Info: Done
[12:14:09] Info: Estimating noise level
[12:14:10] Info: Done
[12:14:14] Info: Clustering molecules...
Progress: 100%|████████████████████████████████████████████████████████████████████████| Time: 0:00:01
  Iteration:                  262
  Max. difference:            0.00729
  Fraction of probs changed:  0.651
[12:14:16] Info: Algorithm stopped after 262 iterations. Max. probability difference: 0.00729. Converged: true.
[12:14:16] Info: Done
[12:14:16] Info: Initializing algorithm. Scale: 36.116947733455746, scale std: 8.876190755101101, initial #components: 32660, #molecules: 48992.
[12:14:17] Info: Using the following additional information about molecules: [:confidence, :cluster, :prior_segmentation]
[12:14:17] Info: Using 3D coordinates
Progress: 100%|████████████████████████████████████████████████████████████████████████| Time: 0:00:14
  Iteration:        500
  Noise level, %:   7.22
  Num. components:  1593
[12:14:32] Info: Processing complete.
[12:14:32] Info: Estimating local colors
[12:14:54] Info: Estimating boundary polygons
Progress: 100%|████████████████████████████████████████████████████████████████████████| Time: 0:00:00
[12:14:55] Info: Saving results to test/segmentation.csv
ERROR: MethodError: no method matching save_segmentation_results(::DataFrames.DataFrame, ::DataFrames.DataFrame, ::SparseArrays.SparseMatrixCSC{Int64, Int64}, ::OrderedCollections.OrderedDict{String, Dict{K, Matrix{Float64}} where K}, ::Baysor.Utils.OutputPaths; matrix_format::Symbol, gene_names::Vector{String}, polygon_format::String)

Closest candidates are:
  save_segmentation_results(::DataFrames.DataFrame, ::DataFrames.DataFrame, ::SparseArrays.SparseMatrixCSC{<:Real, Int64}, ::Union{Nothing, AbstractDict{TI, Matrix{TV}} where {TV<:Real, TI<:Union{Integer, String}}, AbstractDict{String, <:AbstractDict{TI, Matrix{TV}}} where {TV<:Real, TI<:Union{Integer, String}}}, ::Baysor.Utils.OutputPaths; polygon_format, gene_names, matrix_format)
   @ Baysor /home/viktor_petukhov/.julia/dev/Baysor/src/data_loading/cli_wrappers.jl:224

Stacktrace:
 [1] run(coordinates::String, prior_segmentation::String; config::Baysor.Utils.RunOptions, x_column::Symbol, y_column::Symbol, z_column::Symbol, gene_column::Symbol, min_molecules_per_cell::Int64, scale::Float64, scale_std::String, n_clusters::Int64, prior_segmentation_confidence::Float64, output::String, plot::Bool, polygon_format::String, count_matrix_format::String)
   @ Baysor.CommandLine /home/viktor_petukhov/.julia/dev/Baysor/src/cli/main.jl:136
 [2] command_main(ARGS::Vector{String})
   @ Baysor /home/viktor_petukhov/.julia/packages/Comonicon/F3QqZ/src/codegen/julia.jl:343
 [3] command_main
   @ /home/viktor_petukhov/.julia/packages/Comonicon/F3QqZ/src/codegen/julia.jl:90 [inlined]
 [4] julia_main()
   @ Baysor /home/viktor_petukhov/.julia/packages/Comonicon/F3QqZ/src/frontend/cast.jl:481
 [5] top-level scope
   @ none:1

The error seems to be from save_segmentation_results, where few transcripts in one Z level results in ::SparseArrays.SparseMatrixCSC{Int64, Int64}, where the expected input is ::SparseArrays.SparseMatrixCSC{<:Real, Int64}

Would appreciate any help to get this working with all data!