##################################################
## Parameters for step 2 of CUBIC-atlas mapping ##
##################################################
#
#
# Note: to avoid any problems, please do not
#        change the structure of the file
#
#
##########
# Folder #
##########
#
# Output folder directory
/home/Murakami/activity_map/Result
#
# CUBIC-Atlas including folder
/home/Murakami/atlas_folder
#
#
##########################
# Image size information #
##########################
#
# Image size information
/home/Murakami/activity_map/Compress/size_info.csv
#
#
###########################
# Registration parameters #
###########################
#
# The optimization will be performed over three resolution with a maximum of "L" iterations at the coarsest level, "M" at the next coarsest and "N" at the full resolution. For detail, please refer ANTs document (Avants et al., 2011, URL:http://scil.dinf.usherbrooke.ca/wp-content/courses/imn530/ants.pdf). We recommend L = 300, M = 100 and N = 10.
#
# L
300
# M
100
# N
10
#
##############################################################
# Cellular coordinates and downsampled nucleus stained image #
##############################################################
#
# Downsampled nucleus stained image (recommended multi-page tif)
/home/Murakami/activity_map/Compress
#
# CSV file containing list of cell coordinates
/home/Murakami/activity_map/Coordinate
#
# Name of column corresponds to X coordiante
X 
# Name of column corresponds to Y coordiante
Y
# Name of column corresponds to Z coordiante
Slice
# Name of column corresponds to additional information 1
IntDen
# Name of column corresponds to additional information 2
Area
# Name of column corresponds to additional information 3
#
# Name of column corresponds to additional information 4
#
#########
## END ##
#########
