build_traces#
Invoke#
Inside the folder with your input data, run:
pyhim -C build_traces
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.
"tracing_method": ["masking","clustering"], # list of methods it will use
"mask_expansion": 8,# number of pixels masks will be expanded to assign localizations
"masks2process":{"nuclei":"DAPI","mask1":"mask0"}, # masks identities to process
"KDtree_distance_threshold_mum": 1, # threshold distance used for KDtree clustering
Output images:
_XYZ_ROI*.png
full image |
zoomed images |
|
|---|---|---|
3D mask |
|
|
3D mask |
|
|
3D KDtree |
