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MagC_Parameters.txt
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MagC_Parameters.txt
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# MagC parameters
# Lines that start with a single '#' are comment lines
# lines that start with a '##### Plugin' indicate to which plugin the parameters below this line belong
# Lines that do not start with a '#' are parameter lines and should have the following form: 'param = 36' or 'd = 'thePath' or "theList = [3, 6, 'baguette']" .'
##############################
##### Plugin preprocess_ForPipeline #####
##############################
# execute or not the LM and EM parts (1 - True, 0 - False)
executeLM = 1
executeEM = 1
##############################
##### Plugin assembly_LM #####
##############################
# Overlap of the LM patches in the mosaics
overlap = 0.1
# size of the neighborhood for local contrast for the brightfield channel
normLocalContrastSize = 50
# unique identifier for the reference LM channel used for LM alignment and LM/EM registration. The identifier must be contained in the name of the reference channel but not in any other channel
refChannelIdentifier = field
# for contrasting the fluo channels
normLocalContrastSizeFluo = 2000
# for thresholding the fluo channels
minMaxFluo = [15000,65000]
# flip horizontally the LM tiles
flipHorizontally = 1
###########################################
##### Plugin montage_LM #####
###########################################
# mosaic dimension of tiles
mosaic = [2,2]
# fraction of parallel cores used for stitching
fractionCores = 0.1
###########################################
##### Plugin alignRigid_LM #####
###########################################
executeAlignment = 0
# e.g. 0.5, use only the center part of the layer to compute alignment: 0.5 divides the x and y dimensions by 2
boxFactor = 0.5
####################################
##### Plugin export_LMChannels #####
####################################
# assembled LM mosaics will be saved to files with the following scale factors
# /!\ Scalefactor 1 should always be included, as these images are used for LM/EM registration
scaleFactors = [0.1,1]
# flip horizontally the final export for registration
flipX = False
####################################
##### Plugin downsample_EM #####
####################################
cropTiles = 0
downsamplingFactor = 20
nTilesAtATime = 400
normLocalContrastSize = 500
###########################################
##### Plugin montage_Translation #####
###########################################
# Number of layers to montage by each Fiji instance
nLayersAtATime = 2
###########################################
##### Plugin montage_ElasticEM #####
###########################################
# Number of layers to montage by each Fiji instance
nLayersAtATime = 40
nThreads = 20
###########################################
##### Plugin export_stitchedEMForAlignment #####
###########################################
# Number of layers to montage by each Fiji instance
nLayersAtATime = 50
nThreads = 10
################################
##### Plugin alignRigid_EM #####
################################
regModel = 2
###########################################
##### Plugin alignElastic_EM #####
###########################################
# Number of layers to montage by each Fiji instance
layerOverlap = 1
nLayersAtATime = 30
###########################################
##### Plugin export_alignedEMForRegistration #####
###########################################
nLayersAtATime = 40
nThreads = 10
###########################################
##### Plugin compute_RegistrationMovingLeastSquares #####
###########################################
# rejection threshold for the mean displacement of the transforms for the low and high resolution steps, respectively
matchingThreshold = [10,10]
# number of octaves in the SIFT features search at the low and high resolution steps, respectively
nOctaves = [1,4]
# percentage of cropping the EM box for registration. Be careful, the cropped boundaries are then "lost"
cropBoxPercent = 0.1
# on the 8-core computer (zarathustra), more than 6 makes problems when RVS is saving the images (there is a suspicious IJ.openImage in the RVS code ...)
nLayersAtATime = 20