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configuration_octopi_v2.ini
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configuration_octopi_v2.ini
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[GENERAL]
rotate_image_angle = None
flip_image = None
_flip_image_options=[Vertical, Horizontal, Both]
camera_reverse_x = False
_camera_reverse_x_options = [True, False]
camera_reverse_y = False
_camera_reverse_y_options = [True, False]
use_napari_for_live_view = True
use_napari_for_multipoint = True
use_napari_for_tiled_display = True
is_hcs = False
stage_movement_sign_x = -1
stage_movement_sign_y = 1
stage_movement_sign_z = -1
stage_movement_sign_theta = 1
stage_pos_sign_x = -1
stage_pos_sign_y = 1
stage_pos_sign_z = -1
stage_pos_sign_theta = 1
tracking_movement_sign_x = 1
tracking_movement_sign_y = 1
tracking_movement_sign_z = 1
tracking_movement_sign_theta = 1
use_encoder_x = False
_use_encoder_x_options=[True,False]
use_encoder_y = False
_use_encoder_y_options=[True,False]
use_encoder_z = False
_use_encoder_z_options=[True,False]
use_encoder_theta = False
_use_encoder_theta_options=[True,False]
encoder_pos_sign_x = 1
encoder_pos_sign_y = 1
encoder_pos_sign_z = 1
encoder_pos_sign_theta = 1
encoder_step_size_x_mm = 100e-6
encoder_step_size_y_mm = 100e-6
encoder_step_size_z_mm = 100e-6
encoder_step_size_theta = 1
fullsteps_per_rev_x = 200
fullsteps_per_rev_y = 200
fullsteps_per_rev_z = 200
fullsteps_per_rev_theta = 200
screw_pitch_x_mm = 2.54
screw_pitch_y_mm = 2.54
screw_pitch_z_mm = 0.3
microstepping_default_x = 256
microstepping_default_y = 256
microstepping_default_z = 256
microstepping_default_theta = 256
x_motor_rms_current_ma = 1000
y_motor_rms_current_ma = 1000
z_motor_rms_current_ma = 500
x_motor_i_hold = 0.25
y_motor_i_hold = 0.25
z_motor_i_hold = 0.5
max_velocity_x_mm = 25
max_velocity_y_mm = 25
max_velocity_z_mm = 5
max_acceleration_x_mm = 500
max_acceleration_y_mm = 500
max_acceleration_z_mm = 100
scan_stabilization_time_ms_x = 160
scan_stabilization_time_ms_y = 160
scan_stabilization_time_ms_z = 20
homing_enabled_x = True
_homing_enabled_x_options=[True,False]
homing_enabled_y = True
_homing_enabled_y_options=[True,False]
homing_enabled_z = True
_homing_enabled_z_options=[True,False]
sleep_time_s = 0.005
led_matrix_r_factor = 1.8
led_matrix_g_factor = 0.8
led_matrix_b_factor = 0.7
default_saving_path = /Downloads
multipoint_autofocus_channel = BF LED matrix full
multipoint_autofocus_enable_by_default = True
multipoint_bf_saving_option = RGB2GRAY
multipoint_use_piezo_for_zstacks = False
z_stacking_config = FROM CENTER
do_fluorescence_rtp = False
run_custom_multipoint = False
default_display_crop = 90
camera_pixel_size_um = {"IMX226":1.85,"IMX250":3.45,"IMX252":3.45,"PYTHON300":4.8}
objectives = {"2x":{"magnification":2, "NA":0.10, "tube_lens_f_mm":180},"4x":{"magnification":4, "NA":0.13, "tube_lens_f_mm":180}, "10x":{"magnification":10, "NA":0.25, "tube_lens_f_mm":180}, "10x (Mitutoyo)":{"magnification":10, "NA":0.25, "tube_lens_f_mm":200}, "20x (Boli)":{"magnification":20, "NA":0.4, "tube_lens_f_mm":180}, "20x (Nikon)":{"magnification":20, "NA":0.45, "tube_lens_f_mm":200}, "40x":{"magnification":40, "NA":0.6, "tube_lens_f_mm":180}}
tube_lens_mm = 50
camera_sensor = IMX226
_camera_sensor_options=[IMX226,IMX250,IMX252,PYTHON300]
default_objective = 10x (Mitutoyo)
_default_objective_options=[2x,4x,10x,10x (Mitutoyo), 20x (Boli), 20x (Nikon), 40x]
controller_version = Teensy
sort_during_multipoint=False
_sort_during_multipoint_options=[True,False]
disp_th_during_multipoint=0.9
classification_model_path=/home/cephla/Documents/tmp/model_perf_r34_b32.pt
segmentation_model_path=models/m2unet_model_flat_erode1_wdecay5_smallbatch/model_4000_11.pth
classification_test_mode=False
_classification_test_mode_options=[True,False]
segmentation_crop=1500
default_z_pos_mm =6.5
use_trt_segmentation=False
_use_trt_segmentation_options=[True,False]
enable_tracking = False
_enable_tracking_options=[True,False]
[LIMIT_SWITCH_POLARITY]
x_home = 1
y_home = 1
z_home = 0
[PLATE_READER]
number_of_rows = 8
number_of_columns = 12
row_spacing_mm = 9
column_spacing_mm = 9
offset_column_1_mm = 20
offset_row_a_mm = 20
[AF]
stop_threshold = 0.85
crop_width = 800
crop_height = 800
[TRACKING]
search_area_ratio = 10
cropped_img_ratio = 10
bbox_scale_factor = 1.2
default_tracker = csrt
init_methods = ["roi"]
default_init_method = roi
_default_init_method_options = [roi]
trackers = ["csrt", "kcf", "mil", "tld", "medianflow","mosse","daSiamRPN"]
enable_tracking = False
tracking_show_microscope_configurations = False
_tracking_show_microscope_configurations_options = [True,False]
default_display_crop = 100
[ACQUISITION]
crop_width = 3000
crop_height = 3000
number_of_fovs_per_af = 3
image_format = bmp
image_display_scaling_factor = 1.0
dx = 0.9
dy = 0.9
dz = 1.5
[SOFTWARE_POS_LIMIT]
x_positive = 56
x_negative = 0.5
y_positive = 56
y_negative = 0.5
z_positive = 6.5
[SLIDE_POSITION]
loading_x_mm = 30
loading_y_mm = 55
scanning_x_mm = 8
scanning_y_mm = 8