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MosaicPlannerSettingsModel.cfg
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MosaicPlannerSettingsModel.cfg
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[MosaicPlanner]
MM_config_file = string(default="")
MM_database_path = string(default="")
relativemotion = boolean(default = True)
flipvert = boolean(default = True)
transposexy = boolean(default = False)
savetransform = boolean(default = True)
use_focus_correction = boolean(default = False)
default_imagepath = string()
default_arraypath = string()
focal_pos_list_pickle = string(default = "")
autofocus_sleep = float(min=0,default=.2)
autofocus_wait = float(min=0,default=.1)
do_second_autofocus_wait = boolean(default = False)
second_autofocus_wait = float(min=0,default=.4)
hardware_trigger = boolean(default = False)
filter_switch = string(default = None) #should be COM port ID for arduino controlling a filter wheel
microscope_name = string(default = "mosaicplanner")
demoMode = boolean(default = False)
autofocus_toggle = boolean(default = False)
frame_state_save = boolean(default = False)
[Slack]
slack_token = string(default = None)
slack_room = string(default = "general")
notify_list = string(default = "@person1 @person2")
[SSH]
do_ssh_trigger = boolean(default=False)
username = string(default = None)
password = string(default = None)
host = string(default = None)
cron_dir = string(default = None)
timeout = float(default = 15)
[Camera_Settings]
sensor_height = integer(default=2048)
sensor_width = integer(default=2048)
pix_width = float(default=6.5)
pix_height = float(default=6.5)
[ZStackSettings]
zstack_delta = float(default=.3)
zstack_flag = boolean(default=True)
zstack_number = integer(default=5)
[CorrSettings]
CorrTool_window = integer(min = 1,default=100)
CorrTool_delta = integer(min=1,default=75)
CorrTool_skip = integer(default=3)
CorrTool_corr_thresh = float(default=.3)
[SiftSettings]
contrastThreshold = float(default=.3)
numFeatures = integer(min=100,default=1000)
inlier_thresh = integer(min=2,default=12)
[MosaicSettings]
mosaic_mag = float(default=63.0)
mosaic_mx = integer(default =1)
mosaic_my = integer(default =1)
mosaic_overlap = integer(default=10)
mosaic_show_box = boolean(default=True)
mosaic_show_frames = boolean(default =False)
[SmartSEMSettings]
SEM_mag = integer(default =1200)
SEM_tilt = float(default = 0.33)
SEM_rot = float(default = 0.0)
SEM_Z = float(default=0.0125)
SEM_WD = float(default=0.00632568)
[ChannelSettings]
map_chan = string(default='DAPI')
focusscore_chan = string(default='QuadBand1Alexa488')
[MMArduino]
port = string(default='')
interframe_time = integer(default=11)
[LeicaDMI]
port = string(default='')
take_afc_image = boolean(default = False)
[Directories]
Default_Path = string(default='')
Sample_ID = string(default='')
Ribbon_ID = integer(default=0)
Session_ID = integer(default=0)
Map_num = integer(default=0)
Slot_num = integer(default = 0)
meta_experiment_name = string(default = '')
[Software Autofocus]
nonacquisition = integer(default = 35) #number of images to take for software autofocus while outside acquisition loop
acquisition = integer(default = 11) #number of images to take for software autofocus while inside acquisition loop
stepsize = float(default = 0.3) #step size between zplanes, defaults to a +/- 5um range for nonacquisition and +/- 3 um range for acquisition
focus_exp_time = int(default 100) #exposure time to use for software autofocus