G4X output structure

Sample directory tree

---

Directory structure depends on run type.

Transcript & ProteinTranscript

<sample_root>
│
├── diagnostics
│   └── transcript_table.parquet
│
├── g4x_viewer 
│   ├── <sample_1>.bin
│   ├── <sample_1>.ome.tiff              
│   ├── <sample_1>.tar
│   ├── <sample_1>_HE.ome.tiff
│   ├── <sample_1>_nuclear.ome.tiff
│   └── <sample_1>_run_metadata.json
│
├── h_and_e 
│   ├── eosin.jp2
│   ├── eosin_thumbnail.png
│   ├── h_and_e.jp2
│   ├── h_and_e_thumbnail.jpg
│   ├── nuclear.jp2
│   └── nuclear_thumbnail.png
│
├── metrics 
│   ├── core_metrics.csv
│   └── per_area_metrics.csv
│
├── protein                             
│   ├── <protein_1>.jp2
│   ├── <protein_1>_thumbnail.png
│   ├── <protein_2>.jp2
│   ├── <protein_2>_thumbnail.png
│   └── …
│
├── protein_panel.csv                   
│
├── rna
│   └── transcript_table.csv.gz
│
├── run_meta.json
│
├── samplesheet.csv
│
├── segmentation
│   └── segmentation_mask.npz
│
├── single_cell_data
│   ├── cell_by_protein.csv.gz          
│   ├── cell_by_transcript.csv.gz
│   ├── cell_metadata.csv.gz
│   ├── clustering_umap.csv.gz
│   ├── dgex.csv.gz
│   └── feature_matrix.h5
│
├── summary_<sample_1>.html
└── transcript_panel.csv

<sample_root>
│
├── diagnostics
│   └── transcript_table.parquet
│
├── g4x_viewer
│   ├── <sample_1>.bin
│   ├── <sample_1>.tar
│   ├── <sample_1>_HE.ome.tiff
│   ├── <sample_1>_nuclear.ome.tiff
│   └── <sample_1>_run_metadata.json
│
├── h_and_e
│   ├── eosin.jp2
│   ├── eosin_thumbnail.png
│   ├── h_and_e.jp2
│   ├── h_and_e_thumbnail.jpg
│   ├── nuclear.jp2
│   └── nuclear_thumbnail.png
│
├── metrics
│   ├── core_metrics.csv
│   └── per_area_metrics.csv
│
├── rna
│   └── transcript_table.csv.gz
│
├── run_meta.json
│
├── samplesheet.csv
│
├── segmentation
│   └── segmentation_mask.npz
│
├── single_cell_data
│   ├── cell_by_transcript.csv.gz
│   ├── cell_metadata.csv.gz
│   ├── clustering_umap.csv.gz
│   ├── dgex.csv.gz
│   └── feature_matrix.h5
│
├── summary_<sample_1>.html
└── transcript_panel.csv

Sample sub-directory reference

---

root of sample_folder

run_meta.json
samplesheet.csv
summary_<sample_1>.html
transcript_panel.csv
protein_panel.csv (only when protein is included)

diagnostics

transcript_table.parquet

g4x_viewer

<sample_1>.bin
<sample_1>.ome.tiff (only when protein is included)
<sample_1>.tar
<sample_1>_HE.ome.tiff
<sample_1>_nuclear.ome.tiff
<sample_1>_run_metadata.json

h_and_e

eosin.jp2
eosin_thumbnail.png
h_and_e.jp2
h_and_e_thumbnail.jpg
nuclear.jp2
nuclear_thumbnail.png

metrics

core_metrics.csv
per_area_metrics.csv

protein (only when protein is included)

<protein_1>.jp2
<protein_1>_thumbnail.png
<protein_2>.jp2
<protein_2>_thumbnail.png
(additional proteins)

rna

transcript_table.csv.gz

segmentation

segmentation_mask.npz

single_cell_data

cell_by_protein.csv.gz  (only when protein is included)
cell_by_transcript.csv.gz
cell_metadata.csv.gz
clustering_umap.csv.gz
dgex.csv.gz
feature_matrix.h5

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