Parameters#
parameters.json file, previously named infoList.json (DEPRECATED)
Global structure#
Each section in common
represents a step of pyHiM processing. Parameters are defined by default in common
in their corresponding sections. If you want to change a parameter just for one channel, go to labels
and you can overwrite the parameter value in the channel of your choice (an example here).
Parameter overview by section#
Parameters are sort by alphabetical order.
1. acquisition#
Parameter name |
Used to |
---|---|
barcode_channel |
List the files to process; label of barcode channel |
DAPI_channel |
List the files to process; label of DAPI channel |
fiducialBarcode_channel |
List the files to process; label of fiducial channel for barcode cycles |
fiducialDAPI_channel |
List the files to process; label of fiducial channel for the DAPI/RNA cycles |
fiducialMask_channel |
List the files to process; label of fiducial channel for mask cycles |
fileNameRegExp |
Extraction information from filename |
label |
Know which label is currently being processed (added in |
label_channel |
in future this field will contain the ch for the label. This parameter will supersed the individual channel fields above. |
label_channel_fiducial |
in future this field will contain the ch for the label fiducial. This parameter will supersed the individual channel fields above. |
mask_channel |
List the files to process, label of mask channel |
pixelSizeXY |
Get lateral pixel size in nm; compute voxel size for 3D gaussian fitting |
pixelSizeZ |
Get axial pixel size in nm; compute voxel size for 3D gaussian fitting |
RNA_channel |
List the files to process; Label of RNA channel |
zBinning |
Speed up processing time; binning in z-axis. A z-binning of 2 will skip every other plane. A z-binning of 1 will keep all planes. |
2. zProject#
Parameter name |
Used to |
---|---|
blockSize |
Split image into blocks for |
display |
Save output 2D projection as PNG; show image |
folder |
Give a name of output folder to save output data of zPorject features |
mode |
Select projection mode between |
windowSecurity |
Remove the lowest and highest Z-plans for |
zmax |
Set a maximum on Z axis for |
zmin |
Set a minimum on Z axis for |
zProjectOption |
Select projection option between sum of all concerned planes ( |
zwindows |
Set a margin to find best focal place for both |
3. alignImages#
Parameter name |
Used to |
---|---|
alignByBlock |
True will perform block alignment. False will do global alignement. |
background_sigma |
Remove inhomogeneous background; set the number of standard deviations to use for both the lower and upper clipping limit (astropy.stats.SigmaClip) |
blockSize |
Define size in (X,Y) of block for 3D local alignment; value needs to be a power of 2 |
folder |
Give a name of output folder to save output data of register_global features |
higher_threshold |
Set higher threshold to adjust image intensity levels before xcorrelation for |
localAlignment |
Select mode between global alignment ( |
lower_threshold |
Set lower threshold to adjust image intensity levels before xcorrelation for |
outputFile |
Set a base name for output files |
referenceFiducial |
Set name of the reference fiducial cycle |
tolerance |
Determine the % of error tolerated for |
3D_higher_threshold |
Set higher threshold to adjust image intensity levels before xcorrelation for |
3D_lower_threshold |
Set lower threshold to adjust image intensity levels before xcorrelation for |
4. segmentedObjects#
Parameter name |
Used to |
---|---|
area_max |
Set max area to keep 2D segmented object (in pixels) |
area_min |
Set min area to keep 2D segmented object (in pixels) |
background_method |
Select method to process background for |
background_sigma |
Remove inhomogeneous background; set the number of standard deviations to use for both the lower and upper clipping limit (astropy.stats.SigmaClip) |
brightest |
Set max number of objects segmented per FOV (only for barcodes!); “Number of brightest objects to keep after sorting the full object list. If brightest is set to None, all objects will be selected” (photutils.DAOStarFinder) |
centroidDifference_max |
Set max difference between z centroid position determined by moment and by gaussian fitting |
folder |
Give a name of output folder to save output data of segmentedObjects features |
fwhm |
Set source size (in pixels); “The full-width half-maximum (FWHM) of the major axis of the Gaussian kernel in units of pixels.” (photutils.DAOStarFinder) |
intensity_max |
Set max intensity to keep object |
intensity_min |
Set min intensity to keep object |
operation |
Select 2D or 3D method of segmentation for DAPI and barcode label; Process secondary masks in |
outputFile |
Set a base name for output files |
residual_max |
Set maximum difference between axial spot intensity and gaussian fit |
sigma_max |
Set maximum gaussian fit sigma allowed (axial spot intensity) |
stardist_basename |
Set path name of AI models for 2D segmentation with StarDist |
stardist_network |
Set network name for 2D |
stardist_network3D |
Set network name for 3D |
tesselation |
Allow tesselation to segment |
threshold_over_std |
Set threshold used to detect sources |
3D_area_max |
Set max area to keep 3D segmented object (in pixels) |
3D_area_min |
Set min area to keep 3D segmented object (in pixels) |
3D_boxSize |
Set size of box used for block decomposition |
3D_contrast |
“The fraction of the total (blended) source flux that a local peak must have (at any one of the multi-thresholds) to be considered as a separate object.” (photutils.segmentation.deblend_sources) |
3D_lower_threshold |
Set lower threshold for adjusting image levels |
3D_nlevels |
“The number of multi-thresholding levels to use.” (photutils.segmentation.deblend_sources) |
3D_psf_yx |
“Radius of the spot, in nanometer. One value per spatial dimension (zyx or yx dimensions). If it’s a scalar, the same radius is applied to every dimensions.” (apifish.detection.spot_modeling.fit_subpixel) |
3D_psf_z |
“Radius of the spot, in nanometer. One value per spatial dimension (zyx or yx dimensions). If it’s a scalar, the same radius is applied to every dimensions.” (apifish.detection.spot_modeling.fit_subpixel) |
3D_sigma |
instance a 2D Gaussian filter kernel (astropy.convolution.Gaussian2DKernel) |
3D_threshold_over_std |
Set threshold used to detect 3D sources |
3D_higher_threshold |
Set higher threshold for adjusting image levels |
3dAP_brightest |
Set number of sources sought in each YZ plane; “Number of brightest objects to keep after sorting the full object list. If brightest is set to None, all objects will be selected” (photutils.DAOStarFinder) |
3dAP_distTolerance |
Set distance (in pixels) to attribute a source localized in YZ to one localized in XY |
3dAP_flux_min |
Set threshold to keep a source detected in YZ |
3dAP_window |
construct a YZ image by summing from xPlane-window:xPlane+window |
3DGaussianfitWindow |
Set size of window in xy to extract 3D subVolume, in px. 3 means subvolume will be 7x7. |
3Dmethod |
Select which segmentation method to use for the 3D source segmentation between |
5. buildsPWDmatrix#
Parameter name |
Used to |
---|---|
colormaps |
Set colormaps used for plotting matrices |
flux_min |
Set minimum flux per spot for 2D. If flux is smaller, localization will be discarded |
flux_min_3D |
Set minimum flux per spot for 3D localizations. If flux is smaller, localization will be discarded |
folder |
Give a name of output folder to save output data of buildsPWDmatrix features |
KDtree_distance_threshold_mum |
Set distance threshold used to build KDtree |
mask_expansion |
Set number of pixels masks will be expanded to assign localizations |
toleranceDrift |
Set tolerance used for block drift correction (in pixels) |
tracing_method |
Set list of methods it will use |