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EEL Mouse 440 genes single cell data

posted on 2022-09-21, 13:53 authored by Lars BormLars Borm

Cell by gene matrix of the EEL mouse 440 gene experiment.

Single cell data generated by EEL FISH on a saggital mouse brain section. The dataset is available in 3 file formats:

  • .loom Loom file see:
  • .h5ad AnnData file see:
  • .tab Tab-delimited file.


Age - Age of animal.

Codebook - Name of EEL codebook.

ColorDict - Cell cluster color dictionary.

Cycles - Number of barcoding cycles.
Expansion - Pixels the nuceli were expanded (pixelsize = 0.27um).
Expansion_um - Expansion of nuclei in micrometer.
Experiment - Experiment ID.
ExperimentDate - Date of experiment.
FOVoverlapPercentage - Overlap between field of view.
GenerationDate - Loom file generation date.
LOOM_SPEC_VERSION - Loompy version.
MaxHammingDist - maximum allowed Hamming distance.
Operator - Experiment operator.
Orientation - Cutting orientation.
Probes - Probe sequences file.
Protocol - Protocol used.
Quality - Manual evaluation of quality.
RNAfile - RNA file used
Removal - Method of removal of overlapping RNA in overlapping fields of view.
Sample - Sample ID
Segmentation - Segmentation algorithm.
Species - Species of sample.
Stitching - Field of view stitching method.
StitchingChannel - Between cycle alignment channel.
Strain - Strain of animal.
System - Microscope system used.
Tissue - Tissue in experiment.
TotalMolecules - Total number of molecules assigned to cells. 

Column metadata

X - X coordinate in pixels of 0.27um (multiply by 0.27 to get micrometer).

X_um - X coordinate in micrometer.

Y - Y coordinate in pixels of 0.27um (multiply by 0.27 to get micrometer).

Y_um - Y coordinate in micrometer.

tSNE_X - tSNE component 1.

tSNE_Y - tSNE component 2.

Clusters - Cluster label of each cell.

TotalMolecules - Total molecules per cell.

Cluster colors are saved as individual RGB values:

R - Red.

G - Green.

B - Blue.

(In the AnnData file, the tSNE and RGB values are availabe as a single array under "obsm" with keys "tSNE" and "RGB" respectively. )

Row metadata

Gene - Gene name.

GeneTotal - Total number of detected molecules per gene.