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synapseLocatorParams.txt
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synapseLocatorParams.txt
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# Synapse Locator Parameter File, 15jan2020
#
# Synapse Locator directory
synapseLocatorFolder, ''
#
# Elastix File locations
#elastixFolder, elastix\elastix_v4.8
elastixFolder, elastix\elastixProgram
elastixParamsFolder, elastix\elastixParams
elastixParamsSet, default
initialTransformParametersFile, initialTransform_parameters.txt
translationParameterFile, translation_parameters_default.txt
rotationParameterFile, rotation_parameters_default.txt
affineParameterFile, affine_parameters_default.txt
elasticParameterFile, elastic_parameters_default.txt
#
#
# ImageJ program (absolute path)
IJ_exe, C:\fiji.app\ImageJ-win64.exe
#
# ImageJ macros (relative path)
IJMacrosFolder, IJ\IJ1Macros
preprocessMacro, preprocess.ijm
scaleMacro, scaleIt.ijm
featureMakerMacro, featureMaker.ijm
featureMakerSignalChannelMacro, featureMakerSignalChannel.ijm
gatherOutputMacro, gatherTifs.ijm
#
#
# Weka models
# wekaModels directory must contain "SL_genericSpotModel.model" (plus "~_Data.csv") as default model for spots!
wekaModelsFolder, wekaModels
genericSpotModel, SL_genericSpotModel
#
#
# Synapse Locator parameter
leadingChannel, G
loadRegisteredImages, 0
transformRawData, 1
initialTransform, 0
medianFilter, 1
# medianFilterParams, [1.0 1.0 1.0]
medianFilterParams, [1.0 1.0 0.0]
gaussianSmooth, 0
gaussianSmoothParams, [0.5]
bandpassFilter, 1
# bandpassFilterParams, [3 25]
bandpassFilterParams, [2 100]
subtractBackground, 1
subtractBackgroundParams, [250]
deconvolve, 1
# deconvolveParams, [0.01]
deconvolveParams, [0.001]
#deconvolveParams, [1e-10]
deconvolveParams_PSF, [0.4 0.4 2.0]
vxlSize, [0.146 0.146 0.5]
#vxlSize, [0.2 0.2 0.5]
imgSize, [0 0 0]
filterImages, 1
sum2, 0
upsampling, 0
#
#
# Set visually estimated similarity between image stacks {'good', 'average', 'poor'}
apparentSimilarity, average
# Set degree of marker content {'high', 'medium', 'low''}
markerDensity, medium
histogramN, 64
FGSIV, 4
FBSIO, 1
resolutionsN, 3
#
#
# Set registration run mode {'default', 'quick'}
registrationRunMode, default
displayChannel, G0
data1Threshold, 0
data2Threshold, 0
g0_threshold, 0
g1_threshold, 0
bwconncompValue, 26
spotSpecificity, 0.5
signalSpecificity, 0.5
#
#
# Set expected spot size (in pixels)
spotSizeMin, [2 2 1]
spotSizeMax, [10 10 5]
# Set average spot size (in pixels) {'small', 'medium', 'large'}
avgSpotSize, small
# Set dR/G0 label threshold
dRG0Threshold, 0.25
# Exclude spots centered at image stack boundary
excludeSpotsAtEdges, 1
#
#
# Set fields to report in output
#summaryFields, "Spot_ID, row, column, section, spotMatch, spotMatch_probs, Genericmatched, Genericmatched_probs, diameter_x, diameter_y, diameter_z, bb_x, bb_y, bb_z, N, G0_max, R0_max, G1_max, R1_max, G0_sum, R0_sum, G1_sum, R1_sum, G0_mean, R0_mean, G1_mean, R1_mean, G0_median, R0_median, G1_median, R1_median, G0_max_norm, R0_max_norm, G1_max_norm, R1_max_norm, G0_sum_norm, R0_sum_norm, G1_sum_norm, R1_sum_norm, g_ratio, r_ratio, rg_pre, rg_post, r_delta, r_factor, rDelta_gSum, rDelta_g0, g0g1_match, g0r1_match, g1r1_match, g0r0_match, r0r1_match, pval_g0g1, pval_g0r1, pval_g1r1, pval_g0r0, pval_r0r1, VoxelIDs, VoxelIDs2"
summaryFields, "Spot_ID, row, column, section, spotMatch, spotMatch_probs, diameter_x, diameter_y, diameter_z, bb_x, bb_y, bb_z, N, G0_max, R0_max, G1_max, R1_max, G0_sum, R0_sum, G1_sum, R1_sum, G0_mean, R0_mean, G1_mean, R1_mean, G0_median, R0_median, G1_median, R1_median, g_ratio, r_ratio, rg_pre, rg_post, r_delta, r_factor, rDelta_gSum, rDelta_g0, g0g1_match, g0r1_match, g1r1_match, g0r0_match, r0r1_match, edge, outlier, VoxelIDs, VoxelIDs2"
#summaryTableFields, "Spot_ID, row, column, section, G0_max_norm, R0_max_norm, G1_max_norm, R1_max_norm, spotMatch, spotMatch_probs, Genericmatched, Genericmatched_probs, r_factor, rDelta_gSum, rDelta_g0, g_ratio, r_ratio, rg_pre, rg_post, r_delta, diameter_x, diameter_y, diameter_z"
summaryTableFields, "Spot_ID, row, column, section, G0_max, R0_max, G1_max, R1_max, r_factor, rDelta_gSum, rDelta_g0, g_ratio, r_ratio, rg_pre, rg_post, r_delta, diameter_x, diameter_y, diameter_z, spotMatch_probs, g0g1_match, g0r1_match, g1r1_match, g0r0_match, r0r1_match"
compositeTif, 1