-
Notifications
You must be signed in to change notification settings - Fork 8
/
MosaicPlannerSettings.default.cfg
140 lines (110 loc) · 3.3 KB
/
MosaicPlannerSettings.default.cfg
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
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
[SqlAlchemy]
database_path = 'sqlite:///ATdatabase.db'
test_database_path = 'sqlite:///test.db'
#database_path = 'sqlite:///:memory:'
[MosaicPlanner]
MM_config_file = ''
#determines whether or not the positions are moved
#relative to the curvature of the ribbon (True)
#or in euclidean space (False)
relativemotion = True
#whether or not to flip the vertical axis
flipvert = True
#whether or not to transpose the x and y axis
transposexy = False
#whether to save a transformed version of the position list
#when saving a position list (used when making for cross scope position lists)
savetransform = True
#whether to use the focal correction plane when moving in x,y
use_focus_correction = False
default_imagepath = u''
default_arraypath = u''
focal_pos_list_pickle = ''
#how much time in seconds to sleep between requests for autofocus lock
autofocus_sleep = .2
#how much time to wait after finishing an xy move before asking about lock
autofocus_wait = .1
#whether to use hardware triggering of camera exposures and channels
hardware_trigger = False
[Camera_Settings]
#settings describing the size/shape of the camera you will use for acquisition
#height of sensor (pixels)
sensor_height = 2048
#width of sensor (pixels)
sensor_width = 2048
#width/height of pixels (microns)
pix_width = 6.5
pix_height = 6.5
[ZStackSettings]
#microns between z sections
zstack_delta = 0.3
#whether to take a z stack
zstack_flag = False
#number of images in zstack (should be odd to center on current pos)
zstack_number = 5
[CorrSettings]
#size of window to cutout (microns)
CorrTool_window = 100
#size of area to search for match (microns)
CorrTool_delta = 75
#number of pixel locations to skip when searching (for speed)
CorrTool_skip = 3
#pearson correlation coefficent under which the fast forward tool will stop
CorrTool_corr_thresh = 0.3
[SiftSettings]
#the contrast threshold with which to use when searching for keypoints
contrastThreshold = 0.5
#the maximum number of keypoints to use (take top N keypoints in terms of contrast)
numFeatures = 1000
#the number of inliers required in the end to accept a match
#current implementation assumes a rigid transform and a fixed error tolerance
inlier_thresh = 12
[MosaicSettings]
#the magnification to be used in acquiring the final data
mosaic_mag = 63.0
#the number of columns in the mosaic per section
mosaic_mx = 1
#the number of rows in the mosaic per section
mosaic_my = 1
#the percent overlap between frames
mosaic_overlap = 10
#show the individual section bounding boxes
mosaic_show_box = True
#show the individual frame bounding boxes
mosaic_show_frames = False
[SmartSEMSettings]
#settings to control how SmartSEM position list files are saved
#CAUTION,WARNING, CHECK AN EXAMPLE SmartSEM file before using this option
#to be sure the tilt/rot/Z and WD are reasonable for your scope
SEM_mag = 1200
SEM_tilt = 0.33
SEM_rot = 0
SEM_Z = 0.0125
SEM_WD = 0.00632568
[ChannelSettings]
map_chan = '405'
[Transform]
M00 = 1
M01 = 0
M10 = 0
M11 = 1
D0 = 0
D1 = 0
flipvert = False
fliphoriz = False
[StageResetSettings]
enableStageReset = False
focusStage = 'PiezoStage:P:34'
resetStage = 'PiezoStage:P:34'
compensationStage = 'ZStage:Z:32'
minThreshold = -60.0
maxThreshold = 60.0
resetPosition = 0.0
invertCompensation = False
[smtp]
server = ''
port = 0
tls = False
[MMArduino]
port = 'COM10'
interframe_time = 10