localization_analyzer

Reliability status: development

Load a localization table and plot localization quality-control distributions.

The script produces a figure with: - the number of localizations per barcode - the snr distribution per barcode - scatterplot of the snr versus z - scatterplot of roundness versus skew

usage: localization_analyzer [-h] -L LOCALIZATION_FILE [-o OUTPUT_FILE]
                             [-f {png,svg}]

Named Arguments

-L, --localization_file

Localization file path.

-o, --output_file

Output plot file name. Defaults to the name used by LocalizationTable.plot_distribution_fluxes.

-f, --format

Possible choices: png, svg

Output plot format. Default = png.

Default: 'png'

What it does

localization_analyzer loads one localization table and generates a quality-control summary plot for the detected barcode localizations. The plot includes:

  • SNR distribution per barcode.

  • SNR versus z-position scatter plot, colored by object class.

  • Number of detections per barcode.

  • Roundness versus skew scatter plot, colored by barcode.

The input table is read with LocalizationTable.load, so the script supports the same localization formats as the localization table reader, including .ecsv, .dat, and .4dn files.

Usage examples

Create the default PNG output, localization_distribution_fluxes.png:

localization_analyzer \
    --localization_file localizations_3D_barcode.ecsv

Choose an explicit output file:

localization_analyzer \
    --localization_file localizations_3D_barcode.ecsv \
    --output_file qc/localization_qc.png

Save the plot as SVG:

localization_analyzer \
    --localization_file localizations_3D_barcode.ecsv \
    --output_file qc/localization_qc \
    --format svg

Notes

  • --localization_file is required.

  • --format accepts png or svg and defaults to png.

  • When --output_file is omitted, the output is named localization_distribution_fluxes.<format>.

  • If --output_file includes an extension, it is replaced by the selected --format value.