Before Start
Contents
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#
Create a directory with MERFISH experiment name
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.