filter_localizations#
Invoke#
Inside the folder with your input data, run:
pyhim -C filter_localizations
There are several filters:
Properties of 2D localization algorithm (e.g. brightness)
Accuracy of 3D localization: sigma of fit, correlation between z-position from weighted moment and from gaussian fit, etc
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 |
---|---|---|
|
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.