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                                DIRECTORIES
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# input directory, which contains the pictures to be analyzed
input_directory=E:\\morphoJ-bc\\examples\\drug applications\\drugs-hippo\\
output_directory=E:\morphoJ-bc\examples\drug applications\drugs-hippo-db\

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                               IMAGE LOADING
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# file mode by which images should be loaded.
#
# available options:
#
# single:   a single plate defined by a single barcode will be read from the
#           input directory
#
# multiple: a series of barcodes saved in a textfile representing multiple 
#	    plate barcodes will be analyzed
#
# batch:    a series of filenames saved in a textfile representing multiple 
#	    individual images will be analyzed. If multiple colors are used,
#	    the individual color images need to be sorted in order of 
#           analysis.
 
file_mode=single

# file input information - holds the barcode of a single experiment or
# the filename of a textfile (in the input directory) containing a series of 
# barcodes or single image filenames, depending on the file mode choice.

input_info=5a-norm

# the start/end columns and row to be analyzed
start_column=4
end_column=20
start_row=2
end_row=11

positions=3

# for multiple experiment, positions of plates in reference textfile to be
# analyzed
start_plate=1
end_plate=1

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                           MORPHOMETRIC ANALYSIS
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# number of channels to be analyzed
channels=2
channel1=MAP2
channel2=TUJ1

# morphometric measurements to be performed on individual channels all 
# all surements by default. Additional measurements much be activated by
# setting the morphology keyword to 1
#
# morphometric measurements include:
#
# cellbodies: perform morphometric identification of globular/non-filamentous 
#	      structures and perform quantitative measurement of the total
#	      cellbody area per field
#
# neurites:   perform morphometric identification of filamentous structures
#	      and perform quantitative measurement of the total filament
#	      length per field. (requires cellbodies analysis)
#
# endpoints:  perform morphometric identification of filament ends and count
#	      the total number of filament endpoints. Useful for branching
#	      analysis. (requires cellbodies and neurites analyses)
#
# cellcount:  count the total number and average size of cellbody structures.
#	      (requires cellbodies analysis)
#
# each of the morphology keyword is followed by a number representing the 
# channel, for which this analysis should be performed.
# Edit existing values or add more definitions if you use more than 4 channels

# morphometric measurements channel 1

cellbodies1=1
neurites1=1
endpoints1=1
cellcount1=1

# morphometric measurements channel 2

cellbodies2=1
neurites2=1
endpoints2=1
cellcount2=1

# morphometric measurements channel 3

cellbodies3=1
neurites3=0
endpoints3=0
cellcount3=0

# morphometric measurements channel 4

cellbodies4=1
neurites4=1
endpoints4=1
cellcount4=1

# scale values for initial 8-bit conversion of input data

#channel 1
image_scale_min1=200
image_scale_max1=3000

#channel 2
image_scale_min2=300
image_scale_max2=1500

#channel 3
image_scale_min3=200
image_scale_max3=300

#channel 4
image_scale_min4=192
image_scale_max4=316

# size of neurite structure to be detected

#channel 1
neurite_detection_width1=4

#channel 2
neurite_detection_width2=4

#channel 3
neurite_detection_width3=4

#channel 4
neurite_detection_width4=4


# threshold sensitivity of neurite detection

#channel 1
neurite_detection_threshold1=8

#channel 2
neurite_detection_threshold2=8

#channel 3
neurite_detection_threshold3=16

#channel 4
neurite_detection_threshold4=16


# size threshold for exclusion of small objects in the neurite channel

#channel 1
neurite_cleanup_threshold1=50

#channel 2
neurite_cleanup_threshold2=50

#channel 3
neurite_cleanup_threshold3=50

#channel 4
neurite_cleanup_threshold4=50


# threshold sensitivity of neuronal cellbody detection

#channel 1
neuronal_cellbody_detection_threshold1=50

#channel 2
neuronal_cellbody_detection_threshold2=100

#channel 3
neuronal_cellbody_detection_threshold3=50

#channel 4
neuronal_cellbody_detection_threshold4=50

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                             WEB-BASED DATA BROWSER
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# select the inputchannel to derive the trace image to bereported in 
# the web-based data browser
report_channel1=1
report_channel2=1

# select measurements to be included in the web-based data browser

log1name=average_dendrite_length
log1data=average neuritelength1
log2name=average_neurite_length
log2data=average neuritelength2
log3name=dendrites_per_cell
log3data=neurites per cell1
log4name=dendrite_branches_per_length
log4data=branches per neuritelength1
log5name=axon_branches_per_length
log5data=branches per neuritelength2
log6name=MAP2_intensity
log6data=mean intensity1
log7name=TUJ1_intensity
log7data=mean intensity2

# select measurements to be displayed in heatmap/graph measurements

#map1

map1_red=neurite length1
map1_green=cellbody area1
map1_blue=mean intensity1

#map2

map2_red=neurite length2
map2_green=cellbody area2
map2_blue=mean intensity2

#map3

map3_red=neurites per cell1
map3_green=branches per neuritelength1
map3_blue=mean intensity1

#map4

map4_red=neurites per cell2
map4_green=branches per neuritelength2
map4_blue=mean intensity2

end_of_ini