1. Before Start#

1.1. Download test dataset#

A small test dataset used in this user guide can be downloaded from here

1.2. Prepare Your Real Experiment Data#

If you have finished a MERSCOPE run, do the following steps.

1.2.1. Put files in place#

  1. Create a directory with MERFISH experiment name

  2. In this directory, create two sub-directories

    • raw: contains the exact content of the raw dir produced by the machine

    • output: contains region dir produced by the default analysis pipeline

1.2.2. Example#

A real example before any merfishing processing

# Experiment dir
202205231554_MouseSagittalM3S1_VMSC01101/
├── output/
│   └── region_0/
│       ├── 202205231554_MouseSagittalM3S1_VMSC01101_region_0.vzg
│       ├── cell_boundaries/  # contains HDF files for cell boundries
│       ├── cell_by_gene.csv
│       ├── cell_metadata.csv
│       ├── detected_transcripts.csv
│       ├── images/  # contains all the TIFF files for DAPI, PolyT and smFISH, if any
│       └── summary.png
│   └── region_1/
│       ├── ... # your experiment may contains multiple regions if you circled multiple
└── raw/
    ├── data/  # contains the very raw DAX files
    ├── low_resolution/
    ├── seg_preview/
    ├── settings/
    ├── analysis.json
    ├── codebook_0_MouseGene500V1_VA00117.csv  # the codebook used for this experiment
    ├── dataorganization.csv
    ├── EXPERIMENT_FINISHED
    ├── experiment.json
    ├── RAW_DATA_SYNC_FINISHED
    └── settings  # contains the experiment settings

Note

The analysis dir contains intermediate files created by MERLin pipeline from the raw, we don’t archive it.