Index

A

After spotFIT, drop spots that are too close (configuration value)

Aggregate cells prior analysis (configuration value) Analyse until frame number (configuration value)

B

Bounds for sigma in x-direction (configuration value) Bounds for sigma in y-direction (configuration value) Bounds for sigma in z-direction (configuration value)

Bounds for the peak amplitude (configuration value) Bounds for the peak background level (configuration value) Bounds interval for the x and y peak center coord (configuration value) Bounds interval for the z peak center coord (configuration value)

C

Cells segmentation end name (configuration value) Compute reference channel features (configuration value) Compute region properties of the reference channel (configuration value)

Compute spots size (fit gaussian peak(s)) (configuration value) Config YAML filepath (configuration value) Custom combined measurement (configuration value)

D

Disable saving of the final report (configuration value)

E

Experiment folder path(s) to analyse (configuration value)

Extend 3D input segm. objects in Z (configuration value)

F

Features and thresholds for filtering true spots (configuration value) Features for filtering ref. channel objects (configuration value) Features for the size of the saved spots masks (configuration value) File extension of the output tables (configuration value)

Filename of final report (configuration value) filter_spots_from_features_thresholds() (in module spotmax.pipe) Folder path of the final report (configuration value) Folder path of the log file (configuration value)

G

Gaussian filter sigma (configuration value)

I

Initial gaussian filter sigma (configuration value) Initial guess for sigma in x-direction (configuration value) Initial guess for sigma in y-direction (configuration value)

Initial guess for sigma in z-direction (configuration value) Initial guess for the peak amplitude (configuration value) Initial guess for the peak background level (configuration value)

K

Keep external touching objects intact (configuration value)

Keep only spots that are inside ref. channel mask (configuration value)

L

Label components (configuration value)

Local background ring width (configuration value)

M

Maximum number of spot pairs to check (configuration value) Merge spots pairs where single peak fits better (configuration value) Minimum size of spot segmentation mask (configuration value)

Model type (configuration value) module spotmax.pipe

N

Number of frames (SizeT) (configuration value) Number of threads used by numba (configuration value)

Number of z-slices (SizeZ) (configuration value) Numerical aperture (configuration value)

O

Optimise detection for high spot density (configuration value)

P

PhysicalSizeX (configuration value) Pixel height (μm) (configuration value)

Pixel width (μm) (configuration value) Preprocess across experiment (configuration value) Preprocess across timepoints (configuration value)

R

Reduce logging verbosity (configuration value) Ref. channel gaussian filter sigma (configuration value) Ref. channel is single object (e.g., nucleus) (configuration value) Ref. channel segmentation end name (configuration value) Ref. channel segmentation method (configuration value) Ref. channel threshold function (configuration value) Reference channel end name (configuration value)

reference_channel_quantify() (in module spotmax.pipe) reference_channel_semantic_segm() (in module spotmax.pipe) Remove hot pixels (AI input) (configuration value) Remove hot pixels (configuration value) Resolution multiplier in y- and x- direction (configuration value) Resolution multiplier YX (configuration value) Run number (configuration value)

S

Save pre-processed reference channel image (configuration value) Save pre-processed spots image (configuration value) Save prediction map (configuration value) Save reference channel features (configuration value) Save reference channel segmentation masks (configuration value) Save spots segmentation masks (configuration value) Segment reference channel (configuration value) Sharpen spots signal prior detection (configuration value) Sigmas used to enhance network-like structures (configuration value) Skip objects where segmentation failed (configuration value) Spot (z, y, x) minimum dimensions (radius) (configuration value) Spot detection threshold function (configuration value) Spot minimum z-size (μm) (configuration value)

spot_detection() (in module spotmax.pipe) spotfit() (in module spotmax.pipe) spotmax.pipe module Spots channel end name (configuration value) Spots channel segmentation end name (configuration value) Spots coordinates table end name (configuration value) Spots detection method (configuration value) Spots reporter emission wavelength (nm) (configuration value) Spots segmentation method (configuration value) spots_calc_features_and_filter() (in module spotmax.pipe) spots_semantic_segmentation() (in module spotmax.pipe) Stop analysis on critical error (configuration value)

T

Table with lineage info end name (configuration value) Text to append at the end of the output files (configuration value)

Threshold only inside segmented objects (configuration value) Threshold value (configuration value)

U

Use CUDA-compatible GPU (configuration value) Use default values for missing parameters (configuration value)

Use GPU (configuration value) Use the ref. channel mask to determine background (configuration value)

V

Voxel depth (μm) (configuration value)