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Sean Fitzgibbon
SlideR 🍔
Commits
de99b27e
Commit
de99b27e
authored
Aug 03, 2021
by
Sean Fitzgibbon
Browse files
added config with masking
parent
08b9a447
Changes
1
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slider/resources/slide_with_mask.yaml
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de99b27e
header
:
author
:
Istvan N Huszar - adapted by Istvan & Amy Howard Mar 2021 - Adapted by Sean Fitz
2021
description
:
'
'
title
:
TIRL MBP-to-NeuN image registration routine - adapted for histology-to-histology registration
# general settings
general
:
isotropic
:
true
logfile
:
./logfile.log
loglevel
:
debug
name
:
slice-to-slice
outputdir
:
./reg
paramlogfile
:
./paramlog.log
stages
:
-
rotation
-
rigid
-
affine
-
nonlinear
system
:
linux
verbose
:
false
warnings
:
true
# moving image settings
moving
:
dtype
:
f4
export
:
true
file
:
'
'
mask
:
automask
:
thr
:
0.0
uthr
:
1
file
:
null
# function: null
function
:
gmm_mask
normalise
:
true
preview
:
false
resolution_level
:
4
snapshot
:
true
storage
:
mem
# fixed image settings
fixed
:
dtype
:
f4
export
:
false
file
:
'
'
mask
:
automask
:
thr
:
0
uthr
:
1
file
:
null
function
:
gmm_mask
# function: null
normalise
:
true
preview
:
false
resolution_level
:
4
snapshot
:
true
storage
:
mem
# preprocessing settings
preprocessing
:
fixed
:
[
"
fixed_preprocessing"
]
moving
:
[
"
moving_preprocessing"
,
"
match_fixed_resolution"
]
# fixed: null
# moving: ["match_fixed_resolution"]
# registration settings
regparams
:
init
:
scale
:
lb
:
0.95
ub
:
1.05
x0
:
1.0
rotation
:
lb
:
-10
mode
:
deg
ub
:
10
x0
:
0.0
translation
:
x0
:
[
0.0
,
0.0
]
lb
:
[
-5.0
,
-5.0
]
ub
:
[
5.0
,
5.0
]
# restrict lower and upper bound
# lb: [-1.0, -1.0]
# ub: [1.0, 1.0]
affine
:
x0
:
[
1.0
,
0.0
,
0.0
,
0.0
,
1.0
,
0.0
]
lb
:
[
0.95
,
-0.2
,
-1.0
,
-0.2
,
0.95
,
-1.0
]
ub
:
[
1.05
,
0.2
,
1.0
,
0.2
,
1.05
,
1.0
]
nonlinear
:
lb
:
null
ub
:
null
x0
:
0.0
rotsearch
:
coarse
:
1
opt_step
:
0.5
scale
:
0.125
visualise
:
false
xtol_abs
:
[
0.001
,
0.001
,
0.001
,
0.001
]
xtol_rel
:
0.01
export
:
false
snapshot
:
true
rigid
:
opt_step
:
0.1
scaling
:
[
160
,
80
,
40
,
20
,
10
,
5
]
smoothing
:
[
0
,
0
,
0
,
0
,
0
]
visualise
:
false
xtol_abs
:
[
0.001
,
0.001
,
0.001
,
0.001
]
xtol_rel
:
0.01
export
:
false
snapshot
:
true
affine
:
opt_step
:
0.1
scaling
:
[
160
,
80
,
40
,
20
,
10
,
5
]
smoothing
:
[
0
,
0
,
0
,
0
,
0
,
0
,
0
]
visualise
:
false
xtol_abs
:
[
0.001
,
0.001
,
0.001
,
0.001
,
0.001
,
0.001
]
xtol_rel
:
0.01
export
:
false
snapshot
:
true
nonlinear
:
maxiter
:
[
20
,
20
,
20
,
20
,
10
,
10
]
# more regularised
regweight
:
0.4
# regweight: 0.6
scaling
:
[
160
,
80
,
40
,
20
,
10
,
5
]
# scaling: [80, 60, 40, 20, 10, 5]
# can try increasing (1.5, 2, ) number of pixels
# radius of smoothing kernel (number of pixels)
sigma
:
1
smoothing
:
[
0
,
0
,
0
,
0
,
0
,
0
]
truncate
:
1.5
visualise
:
false
# lower will lead to longer registration, might not converge if too small
xtol_abs
:
0.1
xtol_rel
:
0.01
#mm median magnitude
kernel
:
MK_FULL
export
:
true
snapshot
:
true
maskmode
:
or
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