-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathREADME
119 lines (108 loc) · 6.2 KB
/
README
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
Parameter configurations, basic info, terminal calls with parameter configurations.
############################################
#### Neuronchaser ####
############################################
vaa3d -x NeuronChaser -f help
############################################
**** Usage of NeuronChaser tracing ****
vaa3d -x NeuronChaser -f nc_func -i <inimg_file> -p <channel> <scal perc znccTh Ndir angSig Ni Ns zDist saveMidres>
inimg_file The input image\n");
channel Data channel for tracing. Start from 1 (default 1).
scal Scale (5, 20] pix.
perc Percentile [50, 100].
znccTh Correlation threshold [0.5, 1.0).
Ndir nr. directions [5, 20].
angSig Angular sigma [1,90] degs.
Ni nr. iterations [2, 50].
Ns nr. states [1, 20].
zDist z layer dist [1, 4] pix.
saveMidres Save midresults 0-no, 1 -yes.
outswc_file Will be named automatically based on the input image file name, so you don't have to specify it.
############################################
vaa3d -x NeuronChaser -f nc_func -i image.tif -p 1 10 90 0.6 15 60 30 5 1 0
vaa3d -x NeuronChaser -f nc_func -i image.tif -p 1 10 95 0.6 15 60 30 5 1 0
vaa3d -x NeuronChaser -f nc_func -i image.tif -p 1 10 99 0.6 15 60 30 5 1 0
vaa3d -x NeuronChaser -f nc_func -i image.tif -p 1 12 90 0.6 15 60 30 5 1 0
vaa3d -x NeuronChaser -f nc_func -i image.tif -p 1 12 95 0.6 15 60 30 5 1 0
vaa3d -x NeuronChaser -f nc_func -i image.tif -p 1 12 99 0.6 15 60 30 5 1 0
############################################
#### Advantra (bigneuron submission) ####
############################################
vaa3d -x Advantra -f help
############################################
**** Usage of Advantra tracing ****
vaa3d -x Advantra -f advantra_func -i <inimg_file> -p <scal bratio perc znccTh Ndir angSig Ni Ns zDist>
inimg_file The input image
scal Scale (5, 20] pix.
bratio Background ratio (0, 1].
perc Percentile [50, 100].
znccTh Correlation threshold [0.5, 1.0).
Ndir nr. directions [5, 20].
angSig Angular sigma [20,90] degs.
Ni nr. iterations [2, 50].
Ns nr. states [1, 20].
zDist z layer dist [1, 4] pix.
outswc_file Will be named automatically based on the input image file name, so you don't have to specify it.
############################################
vaa3d -x Advantra -f advantra_func -i image.tif -p 10 0.3 95 0.6 15 60 30 5 1
vaa3d -x Advantra -f advantra_func -i image.tif -p 10 0.3 99 0.6 15 60 30 5 1
vaa3d -x Advantra -f advantra_func -i image.tif -p 10 0.8 95 0.6 15 60 30 5 1
vaa3d -x Advantra -f advantra_func -i image.tif -p 10 0.8 99 0.6 15 60 30 5 1
vaa3d -x Advantra -f advantra_func -i image.tif -p 12 0.3 95 0.6 15 60 30 5 1
vaa3d -x Advantra -f advantra_func -i image.tif -p 12 0.3 99 0.6 15 60 30 5 1
vaa3d -x Advantra -f advantra_func -i image.tif -p 12 0.8 95 0.6 15 60 30 5 1
vaa3d -x Advantra -f advantra_func -i image.tif -p 12 0.8 99 0.6 15 60 30 5 1
############################################
#### NeuronChaserX ####
############################################
vaa3d -x NeuronChaserX -f help
############################################
**** Usage of NeuronChaserX ****
vaa3d -x NeuronChaserX -f ncx_func -i <inimg_file> -p <scal bratio perc znccTh Ndir angSig Ni Ns zDist>
inimg_file The input image
scal Scale (5, 20] pix.
bratio Background ratio (0, 1].
perc Percentile [50, 100].
znccTh Correlation threshold [0.5, 1.0).
Ndir nr. directions [5, 20].
angSig Angular sigma [20,90] degs.
Ni nr. iterations [2, 50].
Ns nr. states [1, 20].
zDist z layer dist [1, 4] pix.
outswc_file Will be named automatically based on the input image file name, so you don't have to specify it.
############################################
vaa3d -x NeuronChaserX -f ncx_func -i image.tif -p 10 0.3 95 0.6 15 60 30 5 1
vaa3d -x NeuronChaserX -f ncx_func -i image.tif -p 10 0.3 99 0.6 15 60 30 5 1
vaa3d -x NeuronChaserX -f ncx_func -i image.tif -p 10 0.8 95 0.6 15 60 30 5 1
vaa3d -x NeuronChaserX -f ncx_func -i image.tif -p 10 0.8 99 0.6 15 60 30 5 1
vaa3d -x NeuronChaserX -f ncx_func -i image.tif -p 12 0.3 95 0.6 15 60 30 5 1
vaa3d -x NeuronChaserX -f ncx_func -i image.tif -p 12 0.3 99 0.6 15 60 30 5 1
vaa3d -x NeuronChaserX -f ncx_func -i image.tif -p 12 0.8 95 0.6 15 60 30 5 1
vaa3d -x NeuronChaserX -f ncx_func -i image.tif -p 12 0.8 99 0.6 15 60 30 5 1
############################################
############################################
############################################
On local machine Advantra plugin was replaced with the new Advantra, complete redesign of the bigneuron submission plugin. New code is placed in Advantra directory while the one submitted to the bigneuron was stored in Advantra_bigneuron
############################################
#### Advantra ####
############################################
vaa3d -x Advantra -f help
############################################
---- ADVANTRA usage ----
vaa3d -x Advantra -f advantra_func -i <inimg_file> -p <sigmax msiter sig2radius znccth kappa step ni np zdist>
inimg_file The input image.
sigmax Max Gaussian cross-section sigma.
msiter # refinement iterations.
seedscmin minimum seed score (uint8 greylevels 0-255).
znccth Correlation threshold.
kappa Von Mises variance.
step Prediction step.
ni # trace iterations.
np # trace particles.
zdist z layer dist.
blurring blurring (0-no,1-yes).
grouping grouping method (0-cylinder,1-sphere).
nodepp nodes per pixel trace density limit.
outswc_file Will be named automatically based on the input image file name, so you don't have to specify it.
############################################
~/vaa3d/vaa3d_tools/bin/vaa3d64.app/Contents/MacOS/vaa3d64 -x Advantra -f advantra_func -i image.v3dpbd -p 3 2 0.001 0.4 3 2 20 25 2 0 1 9