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Lucy McNeill
synapsis
Commits
b0be1acd
Commit
b0be1acd
authored
Aug 02, 2021
by
Lucy McNeill
Browse files
coint_foci has option minimum foci
parent
3422fd64
Changes
3
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.DS_Store
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R/count_foci.R
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b0be1acd
...
...
@@ -54,7 +54,7 @@
#' @return foci count per cell
count_foci
<-
function
(
img_path
,
stage
=
"none"
,
offset_px
=
0.2
,
offset_factor
=
2
,
brush_size
=
3
,
brush_sigma
=
3
,
foci_norm
=
0.01
,
annotation
=
"off"
,
channel2_string
=
"SYCP3"
,
channel1_string
=
"MLH3"
,
file_ext
=
"jpeg"
,
KO_str
=
"--"
,
WT_str
=
"++"
,
KO_out
=
"-/-"
,
WT_out
=
"+/+"
,
watershed_stop
=
"off"
,
watershed_radius
=
1
,
watershed_tol
=
0.05
,
crowded_foci
=
TRUE
,
artificial_amp_factor
=
1
,
strand_amp
=
2
,
min_foci
=
9
)
count_foci
<-
function
(
img_path
,
stage
=
"none"
,
offset_px
=
0.2
,
offset_factor
=
2
,
brush_size
=
3
,
brush_sigma
=
3
,
foci_norm
=
0.01
,
annotation
=
"off"
,
channel2_string
=
"SYCP3"
,
channel1_string
=
"MLH3"
,
file_ext
=
"jpeg"
,
KO_str
=
"--"
,
WT_str
=
"++"
,
KO_out
=
"-/-"
,
WT_out
=
"+/+"
,
watershed_stop
=
"off"
,
watershed_radius
=
1
,
watershed_tol
=
0.05
,
crowded_foci
=
TRUE
,
artificial_amp_factor
=
1
,
strand_amp
=
2
,
min_foci
=
1
)
{
cell_count
<-
0
image_count
<
-0
...
...
man/count_foci.Rd
View file @
b0be1acd
...
...
@@ -26,7 +26,7 @@ count_foci(
crowded_foci = TRUE,
artificial_amp_factor = 1,
strand_amp = 2,
min_foci =
9
min_foci =
1
)
}
\arguments{
...
...
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