filter_localizations#

Invoke#

Inside the folder with your input data, run:

pyhim -C filter_localizations

There are several filters:

  1. Properties of 2D localization algorithm (e.g. brightness)

  2. Accuracy of 3D localization: sigma of fit, correlation between z-position from weighted moment and from gaussian fit, etc

  3. Accuracy of drift correction in the region where the barcode was localized.

    This is only applied if LocalDrift correction was not run.

Inputs#

Name shape

Quantity

Mandatory

Description

parameters.json

1

Yes

Parameter file.

Outputs#

Name shape

Quantity

Description

_filtered_barcode_localizations_ROI*.png

Relevant options#

Parameters to run this script will be read from the buildsPWDmatrix field of parameters.json.

"flux_min": 10, # maximum flux allowed for 2D
"flux_min_3D": 4000,# maximum flux allowed for 3D

Output images

Barcode localization statistics

  • _filtered_barcode_localizations_ROI*.png

This provides localization statistics from ASTROPY. The main use of these plots is to determine if the threshold flux used is correct. Default is 200.

In addition, this image displays scatter plots of the flux of each barcode, its sharpness, magnitude and roundness. These are used in order to validate the segmentation process and help with the selection of the flux threshold used in this filtering step.