Add support for multi-modal segmentation #8605

jsicherman · 2024-03-11T22:29:46Z

This adds the ability to read segmentation_method from the cells.zarr.zip for Xenium + multi-modal segmentation datasets. Zarr reading does not seem to be very straightforward with R, though, so some softdepends are needed. An example of this is shown, as well as some demonstrations on how to load other XOA outputs, in a small addition to the spatial vignette.

I also used this opportunity to clean up Xenium reading a bit, and since we will be moving from .csv.gz outputs to exclusively .parquet outputs, added support for that.

jsicherman · 2024-03-11T22:30:59Z

@AustinHartman would be great to also get a review on this PR. Thanks!

pmarks · 2024-04-29T18:02:37Z

@dcollins15 @rsatija ping on this -- what can we do to move this forward?

alikhuseynov · 2024-06-14T14:58:34Z

any updates on this?

rsatija · 2024-07-12T18:58:32Z

Sincere apologies for the delay. We've been slow to respond to PRs but are going to prioritize this going forward. We'll get back to you soon but to confirm, @pmarks you are signed off on this request?

pmarks · 2024-07-12T19:43:26Z

@rsatija thanks for taking a look! Yes, should be ready to go.

rsatija · 2024-07-22T14:24:55Z

Hi @pmarks , sounds great. We're reviewing and just wondering if you could point us to a public dataset for testing, thanks!

pmarks · 2024-07-22T19:43:25Z

Cool! This dataset includes multi-modal segmentation:
https://www.10xgenomics.com/datasets/ffpe-human-pancreas-with-xenium-multimodal-cell-segmentation-1-standard

jsicherman · 2024-08-02T16:23:51Z

Thanks all! Just resolved a conflict that popped up on this branch. Please let me know if there's anything else I can do to help get this reviewed!

jsicherman · 2024-09-13T16:41:21Z

Hi @rsatija @dcollins15, sorry to keep pestering you on this but is there any progress on getting this merged and into a CRAN release? We have quite a few reports of users being blocked in their analyses by the change to transcripts.csv.gz, which would be solved with this PR

Thanks!

rsatija · 2024-09-13T21:17:16Z

Thanks! Agreed that we need to move forward with this. To me, everythign looks good, and I see that you are up-to-date with our develop branch

@dcollins15 if you or the team see any issues here please let @jsicherman know, and if not, we'll go ahead and merge this in a week from today.

SciComp8 · 2024-09-16T00:16:45Z

Hi @rsatija @dcollins15, sorry to keep pestering you on this but is there any progress on getting this merged and into a CRAN release? We have quite a few reports of users being blocked in their analyses by the change to transcripts.csv.gz, which would be solved with this PR

Thanks!

Seems ReadXenium() from the development version of Seurat is incompatible with newly released Xenium 5K data (https://www.10xgenomics.com/datasets/preview-data-xenium-prime-gene-expression)? Any update on loading new Xenium data? Thank you!

alikhuseynov · 2024-09-16T12:28:47Z

Hi @rsatija @dcollins15, sorry to keep pestering you on this but is there any progress on getting this merged and into a CRAN release? We have quite a few reports of users being blocked in their analyses by the change to transcripts.csv.gz, which would be solved with this PR
Thanks!

Seems ReadXenium() from the development version of Seurat is incompatible with newly released Xenium 5K data (https://www.10xgenomics.com/datasets/preview-data-xenium-prime-gene-expression)? Any update on loading new Xenium data? Thank you!

You can use this repo https://github.com/10XGenomics/seurat/tree/develop for now

jsicherman · 2024-09-16T17:07:00Z

Seems ReadXenium() from the development version of Seurat is incompatible with newly released Xenium 5K data (https://www.10xgenomics.com/datasets/preview-data-xenium-prime-gene-expression)? Any update on loading new Xenium data? Thank you!

@ScienceComputing I just confirmed that Seurat::LoadXenium('/path/to/Xenium_Prime_Human_Lymph_Node_Reactive_FFPE') works as expected if you install from the 10XGenomics/develop branch for now (devtools::install_github('10XGenomics/seurat@develop'))

dcollins15

Apologies @jsicherman and @pmarks, I was under the impression that some feedback had been communicated outside of this thread, it wasn't my intent to leave you hanging!

Aside from one last copy-paste error, things seem to be working as expected with the Human Lung Cancer and Human Pancreas datasets. Unfortunately, I'm still unable to parse the older Mouse Brain Coronal Subset data (see comments below).

Once everything is working, there are a few documentation-related tasks to handle before this can be safely merged:

stars and (maybe) gmp should be added to the DESCRIPTION under Suggests (i.e., listed as a suggested dependency)
The @importFrom utils unzip tag needs to be added to the docstring for ReadXenium
The NAMESPACE and man/*.Rd files need to be updated — this can be done using roxygen2::roxygenise or devtools::document
An entry should be added to the NEWS.md file describing the changes introduced in this PR. The more detail provided in the changelog, the better for users

After those are taken care of, the final step is to bump the devel version and date in the DESCRIPTION file. Since another change is just about ready to be merged, I expect this will land as v5.1.0.9006 🚀

R/preprocessing.R

vignettes/seurat5_spatial_vignette_2.Rmd

R/preprocessing.R

jsicherman · 2024-09-20T04:46:47Z

Thanks for the thorough review @dcollins15! Will try to put up some fixes on Monday. Should be able to remove the softdepends on gmp, stars and jsonlite, as some things changed in the outputs between when I put this up and now to simplify this integration.

SciComp8 · 2024-09-23T01:12:33Z

@ScienceComputing

Thank you so much for the updates. I tried the new dev version of Seurat, but the Xenium 5K data still cannot be loaded normally. Any insights on this issue?

Error: file not found
In addition: Warning message:
In CPL_read_mdim(file, array_name, options, offset, count, step, :
GDAL Error 1: Decompressor blosc not handled

> data.path <- 'Xenium_Prime_Human_Lymph_Node_Reactive_FFPE_outs'
> list.files(data.path)
 [1] "analysis_summary.html"                                            
 [2] "analysis.tar.gz"                                                  
 [3] "analysis.zarr.zip"                                                
 [4] "aux_outputs.tar.gz"                                               
 [5] "cell_boundaries.csv.gz"                                           
 [6] "cell_boundaries.parquet"                                          
 [7] "cell_feature_matrix.h5"                                           
 [8] "cell_feature_matrix.tar.gz"                                       
 [9] "cell_feature_matrix.zarr.zip"                                     
[10] "cells.csv.gz"                                                     
[11] "cells.parquet"                                                    
[12] "cells.zarr.zip"                                                   
[13] "experiment.xenium"                                                
[14] "gene_panel.json"                                                  
[15] "metrics_summary.csv"                                              
[16] "morphology_focus"                                                 
[17] "morphology.ome.tif"                                               
[18] "nucleus_boundaries.csv.gz"                                        
[19] "nucleus_boundaries.parquet"                                       
[20] "transcripts.parquet"                                              
[21] "transcripts.zarr.zip"                                             
[22] "Xenium_Prime_Human_Lymph_Node_Reactive_FFPE_cell_types.csv"       
[23] "Xenium_Prime_Human_Lymph_Node_Reactive_FFPE_gene_groups.csv"      
[24] "Xenium_Prime_Human_Lymph_Node_Reactive_FFPE_he_image.ome.tif"     
[25] "Xenium_Prime_Human_Lymph_Node_Reactive_FFPE_he_imagealignment.csv"

> xenium.obj <- Seurat::LoadXenium(data.dir=data.path)
Error: file not found
In addition: Warning message:
In CPL_read_mdim(file, array_name, options, offset, count, step,  :
  GDAL Error 1: Decompressor blosc not handled

> sessionInfo()
R version 4.4.0 (2024-04-24)
Platform: aarch64-apple-darwin20
Running under: macOS Ventura 13.3

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] progressr_0.14.0   jsonlite_1.8.9     gmp_0.7-5          stars_0.6-6       
[5] sf_1.0-17          abind_1.4-5        Seurat_5.1.0.9004  SeuratObject_5.0.2
[9] sp_2.1-3          

loaded via a namespace (and not attached):
  [1] RColorBrewer_1.1-3     rstudioapi_0.16.0      magrittr_2.0.3        
  [4] spatstat.utils_3.1-0   fs_1.6.4               vctrs_0.6.5           
  [7] ROCR_1.0-11            memoise_2.0.1          spatstat.explore_3.2-7
 [10] htmltools_0.5.8.1      usethis_2.2.3          sctransform_0.4.1     
 [13] parallelly_1.37.1      KernSmooth_2.23-22     htmlwidgets_1.6.4     
 [16] ica_1.0-3              plyr_1.8.9             plotly_4.10.4         
 [19] zoo_1.8-12             cachem_1.0.8           igraph_2.0.3          
 [22] mime_0.12              lifecycle_1.0.4        pkgconfig_2.0.3       
 [25] Matrix_1.7-0           R6_2.5.1               fastmap_1.1.1         
 [28] fitdistrplus_1.1-11    future_1.33.2          shiny_1.8.1.1         
 [31] digest_0.6.35          colorspace_2.1-0       patchwork_1.2.0       
 [34] tensor_1.5             RSpectra_0.16-1        irlba_2.3.5.1         
 [37] pkgload_1.3.4          fansi_1.0.6            spatstat.sparse_3.0-3 
 [40] httr_1.4.7             polyclip_1.10-6        compiler_4.4.0        
 [43] proxy_0.4-27           remotes_2.5.0          DBI_1.2.2             
 [46] fastDummies_1.7.3      pkgbuild_1.4.4         MASS_7.3-60.2         
 [49] sessioninfo_1.2.2      classInt_0.4-10        tools_4.4.0           
 [52] units_0.8-5            lmtest_0.9-40          httpuv_1.6.15         
 [55] future.apply_1.11.2    goftest_1.2-3          glue_1.7.0            
 [58] nlme_3.1-164           promises_1.3.0         grid_4.4.0            
 [61] Rtsne_0.17             cluster_2.1.6          reshape2_1.4.4        
 [64] generics_0.1.3         gtable_0.3.5           spatstat.data_3.0-4   
 [67] class_7.3-22           tidyr_1.3.1            data.table_1.15.4     
 [70] utf8_1.2.4             spatstat.geom_3.2-9    RcppAnnoy_0.0.22      
 [73] ggrepel_0.9.5          RANN_2.6.1             pillar_1.9.0          
 [76] stringr_1.5.1          spam_2.10-0            RcppHNSW_0.6.0        
 [79] later_1.3.2            splines_4.4.0          dplyr_1.1.4           
 [82] lattice_0.22-6         survival_3.5-8         deldir_2.0-4          
 [85] tidyselect_1.2.1       miniUI_0.1.1.1         pbapply_1.7-2         
 [88] gridExtra_2.3          scattermore_1.2        devtools_2.4.5        
 [91] matrixStats_1.3.0      stringi_1.8.3          lazyeval_0.2.2        
 [94] codetools_0.2-20       tibble_3.2.1           cli_3.6.2             
 [97] uwot_0.2.2             xtable_1.8-4           reticulate_1.36.1     
[100] munsell_0.5.1          Rcpp_1.0.12            globals_0.16.3        
[103] spatstat.random_3.2-3  png_0.1-8              parallel_4.4.0        
[106] ellipsis_0.3.2         ggplot2_3.5.1          dotCall64_1.1-1       
[109] profvis_0.3.8          urlchecker_1.0.1       listenv_0.9.1         
[112] viridisLite_0.4.2      scales_1.3.0           ggridges_0.5.6        
[115] e1071_1.7-14           leiden_0.4.3.1         purrr_1.0.2           
[118] rlang_1.1.3            cowplot_1.1.3

alikhuseynov · 2024-09-23T11:30:42Z

CPL_read_mdim

seems to be related ->
r-spatial/stars#663 (comment)
do you have recent GDAL version? eg:

gdalinfo --version
GDAL 3.9.0, released 2024/05/07

SciComp8 · 2024-09-24T14:41:07Z

CPL_read_mdim

seems to be related -> r-spatial/stars#663 (comment) do you have recent GDAL version? eg:
gdalinfo --version
GDAL 3.9.0, released 2024/05/07

Yes, I do have the newly released GDAL. What’s the next step I should take to successfully load the data? Highly appreciate your help and time.

gdalinfo --version
GDAL 3.9.2, released 2024/08/13

jsicherman · 2024-09-24T18:02:17Z

@ScienceComputing try re-installing (devtools::install_github("10XGenomics/seurat@develop", force = TRUE)) and re-attempting your call. I have updated it to not read the cells.zarr.zip in favor of the cells.csv.gz file, which should naturally resolve this issue.

@dcollins15 let me know if you want me to tackle these on this PR or if that's something you'd rather have your team manage. Changelog below.

The NAMESPACE and man/*.Rd files need to be updated — this can be done using roxygen2::roxygenise or devtools::document
An entry should be added to the NEWS.md file describing the changes introduced in this PR. The more detail provided in the changelog, the better for users

Improved: more fine-grained control over what parts of a Xenium experiment are loaded in LoadXenium
Added: ability to load Xenium nucleus segmentation masks
Added: read additional feature types from Xenium experiments
Added: read some run metadata (run start time, preservation method, panel used, organism, tissue type, instrument software version and stain kit used)
Improved: read cell_feature_matrix.h5 when present in favor of the MEX format files
Improved: more robust output/error handling in ReadXenium
Added: ability to read segmentation_method directly into Xenium meta.data
Added/fixed: ability to read .parquet files using arrow
Added: vignette for reading a Xenium dataset with the cell segmentation kit

YfCem · 2024-09-25T10:18:41Z

Thank you so much for the updates! I've been really looking forward to this to be able to analyze my Xenium data. (multi tissue Mouse panel + 100 custom genes)
This is probably a rookie question, but when I try to load my data I get the following error. Any ideas?

Error in CreateAssayObject():
! No cell names (colnames) names present in the input matrix

list.files(path)
 [1] "analysis"                     "analysis.zarr.zip"           
 [3] "analysis_summary.html"        "aux_outputs"                 
 [5] "cell_boundaries.csv.gz"       "cell_boundaries.parquet"     
 [7] "cell_feature_matrix"          "cell_feature_matrix.h5"      
 [9] "cell_feature_matrix.zarr.zip" "cells.csv"                   
[11] "cells.csv.7z"                 "cells.csv.gz"                
[13] "cells.parquet"                "cells.zarr.zip"              
[15] "experiment.xenium"            "gene_panel.json"             
[17] "metrics_summary.csv"          "morphology.ome.tif"          
[19] "morphology_focus"             "nucleus_boundaries.csv.gz"   
[21] "nucleus_boundaries.parquet"   "transcripts.parquet"         
[23] "transcripts.zarr.zip"     

 xenium.obj <- LoadXenium(path)
  Genome matrix has multiple modalities, returning a list of matrices for this genome
Error in `CreateAssayObject()`:
! No cell names (colnames) names present in the input matrix
Backtrace:
    ▆
 1. └─Seurat::LoadXenium(...)
 2.   └─SeuratObject::CreateAssayObject(counts = data$matrix[[name]])
 3.     └─rlang::abort(message = "No cell names (colnames) names present in the input matrix")
 
 sessionInfo()
R version 4.4.1 (2024-06-14 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 10 x64 (build 19045)

Matrix products: default


locale:
[1] LC_COLLATE=English_United Kingdom.utf8  LC_CTYPE=English_United Kingdom.utf8   
[3] LC_MONETARY=English_United Kingdom.utf8 LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.utf8    

time zone: Europe/Berlin
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] ggplot2_3.5.1      future_1.34.0      Seurat_5.1.0.9004  SeuratObject_5.0.2
[5] sp_2.1-4          

loaded via a namespace (and not attached):
  [1] RColorBrewer_1.1-3     rstudioapi_0.16.0      jsonlite_1.8.9        
  [4] magrittr_2.0.3         spatstat.utils_3.1-0   farver_2.1.2          
  [7] fs_1.6.4               vctrs_0.6.5            ROCR_1.0-11           
 [10] memoise_2.0.1          spatstat.explore_3.3-2 htmltools_0.5.8.1     
 [13] usethis_3.0.0          curl_5.2.2             sctransform_0.4.1     
 [16] parallelly_1.38.0      KernSmooth_2.23-24     htmlwidgets_1.6.4     
 [19] desc_1.4.3             ica_1.0-3              plyr_1.8.9            
 [22] plotly_4.10.4          zoo_1.8-12             cachem_1.1.0          
 [25] igraph_2.0.3           mime_0.12              lifecycle_1.0.4       
 [28] pkgconfig_2.0.3        Matrix_1.7-0           R6_2.5.1              
 [31] fastmap_1.2.0          fitdistrplus_1.2-1     shiny_1.9.1           
 [34] digest_0.6.37          colorspace_2.1-1       patchwork_1.3.0       
 [37] ps_1.8.0               tensor_1.5             RSpectra_0.16-2       
 [40] irlba_2.3.5.1          pkgload_1.4.0          progressr_0.14.0      
 [43] fansi_1.0.6            spatstat.sparse_3.1-0  httr_1.4.7            
 [46] polyclip_1.10-7        abind_1.4-8            compiler_4.4.1        
 [49] remotes_2.5.0          withr_3.0.1            bit64_4.0.5           
 [52] fastDummies_1.7.4      pkgbuild_1.4.4         R.utils_2.12.3        
 [55] MASS_7.3-60.2          sessioninfo_1.2.2      tools_4.4.1           
 [58] lmtest_0.9-40          httpuv_1.6.15          future.apply_1.11.2   
 [61] goftest_1.2-3          R.oo_1.26.0            glue_1.7.0            
 [64] callr_3.7.6            nlme_3.1-164           promises_1.3.0        
 [67] grid_4.4.1             Rtsne_0.17             cluster_2.1.6         
 [70] reshape2_1.4.4         generics_0.1.3         hdf5r_1.3.11          
 [73] gtable_0.3.5           spatstat.data_3.1-2    tzdb_0.4.0            
 [76] R.methodsS3_1.8.2      tidyr_1.3.1            data.table_1.16.0     
 [79] utf8_1.2.4             spatstat.geom_3.3-3    RcppAnnoy_0.0.22      
 [82] ggrepel_0.9.6          RANN_2.6.2             pillar_1.9.0          
 [85] stringr_1.5.1          spam_2.10-0            RcppHNSW_0.6.0        
 [88] later_1.3.2            splines_4.4.1          dplyr_1.1.4           
 [91] lattice_0.22-6         survival_3.6-4         bit_4.0.5             
 [94] deldir_2.0-4           tidyselect_1.2.1       miniUI_0.1.1.1        
 [97] pbapply_1.7-2          gridExtra_2.3          scattermore_1.2       
[100] devtools_2.4.5         matrixStats_1.4.1      stringi_1.8.4         
[103] lazyeval_0.2.2         codetools_0.2-20       tibble_3.2.1          
[106] cli_3.6.3              uwot_0.2.2             arrow_17.0.0.1        
[109] xtable_1.8-4           reticulate_1.39.0      munsell_0.5.1         
[112] processx_3.8.4         Rcpp_1.0.13            globals_0.16.3        
[115] spatstat.random_3.3-2  png_0.1-8              spatstat.univar_3.0-1 
[118] parallel_4.4.1         ellipsis_0.3.2         assertthat_0.2.1      
[121] dotCall64_1.1-1        profvis_0.3.8          urlchecker_1.0.1      
[124] listenv_0.9.1          viridisLite_0.4.2      scales_1.3.0          
[127] ggridges_0.5.6         leiden_0.4.3.1         purrr_1.0.2           
[130] rlang_1.1.4            cowplot_1.1.3

jsicherman · 2024-09-25T16:30:49Z

@YfCem Were any edits made to the contents of cell_feature_matrix/ in your outs folder? If you do...

fread(file.path(path, 'cell_feature_matrix', 'features.tsv.gz'), header = FALSE)

You should see cell IDs. This error would suggest to me that, for some reason, that file is empty? Though admittedly I haven't dug around in the code to load the MEX outputs too much.

YfCem · 2024-09-25T18:16:45Z

@jsicherman Thanks for getting back to me so quick! I gave your recommendation a try and this is what I got:

fread(file.path(path, 'cell_feature_matrix', 'features.tsv.gz'), header = FALSE)
                          V1                      V2                        V3
                      <char>                  <char>                    <char>
  1:      ENSMUSG00000109644           0610005C13Rik           Gene Expression
  2:      ENSMUSG00000028441           1110017D15Rik           Gene Expression
  3:      ENSMUSG00000096001           2610528A11Rik           Gene Expression
  4:      ENSMUSG00000040412           5330417C22Rik           Gene Expression
  5:      ENSMUSG00000018451           6330403K07Rik           Gene Expression
 ---                                                                          
537: NegControlCodeword_0537 NegControlCodeword_0537 Negative Control Codeword
538: NegControlCodeword_0538 NegControlCodeword_0538 Negative Control Codeword
539: NegControlCodeword_0539 NegControlCodeword_0539 Negative Control Codeword
540: NegControlCodeword_0540 NegControlCodeword_0540 Negative Control Codeword
541: UnassignedCodeword_0020 UnassignedCodeword_0020       Unassigned Codeword

I'm interpreting this as the file is not empty?

Appreciate all the help!

alikhuseynov · 2024-09-25T19:27:54Z

CPL_read_mdim

seems to be related -> r-spatial/stars#663 (comment) do you have recent GDAL version? eg:
gdalinfo --version
GDAL 3.9.0, released 2024/05/07
Yes, I do have the newly released GDAL. What’s the next step I should take to successfully load the data? Highly appreciate your help and time.
gdalinfo --version
GDAL 3.9.2, released 2024/08/13

Probably it is now solved with the latest commits.
However if you want to try out Bioconductor stuff, here would be the example -> SFE_xenium, btw image can be loaded too for visualization and/or some image analysis

dcollins15 · 2024-09-25T21:21:16Z

Thanks for getting these updates pushed up so quickly, @jsicherman! I'll have another round of comments ready for you tomorrow 👌

To answer your question — ideally, the NAMESPACE, man/*.Rd, and NEWS.md updates should be made before this PR is merged. I'd be happy to take care of the final updates once the other changes are ready, but I don't think I have write access to the 10XGenomics/seruat:develop branch.

I'll also take a stab at refining the changelog you provided to ensure consistency — we appreciate you getting it started 🙏

In general, things are looking sweet! Excited to get this functionality merged and released 🤓

SciComp8 · 2024-09-25T21:38:17Z

@ScienceComputing try re-installing (devtools::install_github("10XGenomics/seurat@develop", force = TRUE)) and re-attempting your call. I have updated it to not read the cells.zarr.zip in favor of the cells.csv.gz file, which should naturally resolve this issue.

@dcollins15 let me know if you want me to tackle these on this PR or if that's something you'd rather have your team manage. Changelog below.

The NAMESPACE and man/*.Rd files need to be updated — this can be done using roxygen2::roxygenise or devtools::document
An entry should be added to the NEWS.md file describing the changes introduced in this PR. The more detail provided in the changelog, the better for users

Improved: more fine-grained control over what parts of a Xenium experiment are loaded in LoadXenium

Added: ability to load Xenium nucleus segmentation masks

Added: read additional feature types from Xenium experiments

Added: read some run metadata (run start time, preservation method, panel used, organism, tissue type, instrument software version and stain kit used)

Improved: read cell_feature_matrix.h5 when present in favor of the MEX format files

Improved: more robust output/error handling in ReadXenium

Added: ability to read segmentation_method directly into Xenium meta.data

Added/fixed: ability to read .parquet files using arrow

Added: vignette for reading a Xenium dataset with the cell segmentation kit

Thank you so much for your wonderful updates! It works!

SciComp8 · 2024-09-25T21:43:57Z

CPL_read_mdim

seems to be related -> r-spatial/stars#663 (comment) do you have recent GDAL version? eg:
gdalinfo --version
GDAL 3.9.0, released 2024/05/07
Yes, I do have the newly released GDAL. What’s the next step I should take to successfully load the data? Highly appreciate your help and time.
gdalinfo --version
GDAL 3.9.2, released 2024/08/13
Probably it is now solved with the latest commits. However if you want to try out Bioconductor stuff, here would be the example -> SFE_xenium, btw image can be loaded too for visualization and/or some image analysis

Yes, the Xenium 5K data works well with your team's latest commits. Thank you sooo much for your amazing help & suggestion. Absolutely, would like to give it try!

dcollins15

LGTM 🚀 thanks for all your patience @jsicherman

I've got one small error-handling nit below — it's non-blocking and easy for us to address in quick follow-up PR, so I'll let you decide if it's worth adjusting now 😄

Just a heads-up: none of the datasets I've been using appear to have the segmentation_method column in either of the cells.csv.gz" or cells.parquet files. It's entirely possible I might have pulled down the wrong versions...

The last piece of housekeeping is to bump the version and date in the DESCRIPTION file and then I'll merge this in as v5.1.0.9006 🥳

R/convenience.R

R/preprocessing.R

dcollins15 · 2024-09-26T17:56:33Z

vignettes/seurat5_spatial_vignette_2.Rmd

+We can directly visualize cells which were segmented according to each method.
+
+```{r}
+ImageDimPlot(xenium.obj, fov = "fov", dark.background = F, group.by = "segmentation_method", cols = c('#ffabc3', '#a9a900', '#a9ceff'))


Non-blocking but this line is throwing an error because of the missing meta.data column. We need to make some other updates to this vignette before our next release so we can make any required adjustments then.

NEWS.md

jsicherman · 2024-09-29T22:41:05Z

Thanks @dcollins15! Appreciate the discussion on the PR 🚀 !

jsicherman added 5 commits February 28, 2024 17:16

add arrow support and ability to read zarr

3dad59d

wwip

b3a4c01

clean up the API a bit

d55be3a

bulk out vignette

8739625

feat(xenium): arrow support and XOA updates

4ec45ef

jsicherman mentioned this pull request Mar 11, 2024

small fix for ReadXenium #8298

Closed

jsicherman added 2 commits March 18, 2024 16:13

cleaner errors for missing files/arrow

e0ad8f1

chore: cleaner error for missing files/dependencies

5ed3ef1

doc: update some documentation (#7)

ae06169

alikhuseynov mentioned this pull request Jun 23, 2024

Major changes on Xenium v3 output files #9035

Open

fix: load genomic controls when present

a9ca7f0

Merge branch 'develop' into develop

b4af762

jsicherman mentioned this pull request Aug 7, 2024

Xenium support #6440

Merged

5 tasks

jsicherman mentioned this pull request Aug 26, 2024

New Xenium output bundle not compatible with ReadXenium() - no more transcripts.csv.gz #9060

Open

Merge branch 'develop' into develop

a6beb37

Typo

41adcb4

dcollins15 requested changes Sep 18, 2024

View reviewed changes

R/preprocessing.R Outdated Show resolved Hide resolved

R/preprocessing.R Outdated Show resolved Hide resolved

vignettes/seurat5_spatial_vignette_2.Rmd Show resolved Hide resolved

R/preprocessing.R Outdated Show resolved Hide resolved

jsicherman added 3 commits September 18, 2024 10:28

fix: copypasta on nucleus_boundaries

23a2037

fix: don't load segmentation method on old datasets

7454eb0

fix: read cells.parquet or csv.gz instead of zarr.zip

fb04354

fix: parse arrow binary type

efcb507

docs: update vignette

d362ba0

jsicherman added 2 commits September 25, 2024 15:47

doc: update NEWS and roxygenize

0c536c7

Merge branch 'develop' into develop

5ebdf44

dcollins15 approved these changes Sep 26, 2024

View reviewed changes

fix: better error handling

db8bd41

dcollins15 merged commit 63a7b1a into satijalab:develop Sep 30, 2024
1 check failed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Add support for multi-modal segmentation #8605

Add support for multi-modal segmentation #8605

jsicherman commented Mar 11, 2024

jsicherman commented Mar 11, 2024

pmarks commented Apr 29, 2024

alikhuseynov commented Jun 14, 2024

rsatija commented Jul 12, 2024

pmarks commented Jul 12, 2024

rsatija commented Jul 22, 2024

pmarks commented Jul 22, 2024

jsicherman commented Aug 2, 2024

jsicherman commented Sep 13, 2024

rsatija commented Sep 13, 2024

SciComp8 commented Sep 16, 2024

alikhuseynov commented Sep 16, 2024

jsicherman commented Sep 16, 2024

dcollins15 left a comment

jsicherman commented Sep 20, 2024

SciComp8 commented Sep 23, 2024 •

edited

Loading

alikhuseynov commented Sep 23, 2024

SciComp8 commented Sep 24, 2024

jsicherman commented Sep 24, 2024

YfCem commented Sep 25, 2024

jsicherman commented Sep 25, 2024

YfCem commented Sep 25, 2024

alikhuseynov commented Sep 25, 2024

dcollins15 commented Sep 25, 2024

SciComp8 commented Sep 25, 2024

SciComp8 commented Sep 25, 2024

dcollins15 left a comment

dcollins15 Sep 26, 2024

jsicherman commented Sep 29, 2024

Add support for multi-modal segmentation #8605

Add support for multi-modal segmentation #8605

Conversation

jsicherman commented Mar 11, 2024

jsicherman commented Mar 11, 2024

pmarks commented Apr 29, 2024

alikhuseynov commented Jun 14, 2024

rsatija commented Jul 12, 2024

pmarks commented Jul 12, 2024

rsatija commented Jul 22, 2024

pmarks commented Jul 22, 2024

jsicherman commented Aug 2, 2024

jsicherman commented Sep 13, 2024

rsatija commented Sep 13, 2024

SciComp8 commented Sep 16, 2024

alikhuseynov commented Sep 16, 2024

jsicherman commented Sep 16, 2024

dcollins15 left a comment

Choose a reason for hiding this comment

jsicherman commented Sep 20, 2024

SciComp8 commented Sep 23, 2024 • edited Loading

alikhuseynov commented Sep 23, 2024

SciComp8 commented Sep 24, 2024

jsicherman commented Sep 24, 2024

YfCem commented Sep 25, 2024

jsicherman commented Sep 25, 2024

YfCem commented Sep 25, 2024

alikhuseynov commented Sep 25, 2024

dcollins15 commented Sep 25, 2024

SciComp8 commented Sep 25, 2024

SciComp8 commented Sep 25, 2024

dcollins15 left a comment

Choose a reason for hiding this comment

dcollins15 Sep 26, 2024

Choose a reason for hiding this comment

jsicherman commented Sep 29, 2024

SciComp8 commented Sep 23, 2024 •

edited

Loading