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config.yaml
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config.yaml
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user_config:
# Quick configuration group for LSM
exposure-level : "high"
# 'low' -> scan rate: '500000.0000', pockel cell gain: 0.30, PMT gain: 0.40
# 'mid' -> scan rate: '400000.0000', pockel cell gain: 0.45, PMT gain: 0.45
# 'high' -> scan rate: '250000.0000', pockel cell gain: 0.60, PMT gain: 0.50
# 'extreme' -> scan rate: '200000.0000', pockel cell gain: 0.75, PMT gain: 0.55
snr-level : "low"
# Estimiated correction according to sample SNR level. Available value: 'low', 'mid', 'high', by default raw data is collected
autofocus-speed : 3
# Speed of software autofocus, integer: 1~5. Bigger value leads to faster brightfield scan but potentially lower autofocus performance
lsm-resolution : 256
# LSM scan resolution, available resolution: 256, 512, 1024
lsm-bin-factor : 15
# LSM scan pixel average factor, positive integer
lsm-scan-rate : "250000.0000"
# LSM scan rate, available value (string): '125000.0000', '200000.0000', '250000.0000','400000.0000', '500000.0000', '625000.0000', '1000000.0000'
lsm-pc-power : 0.4
# LSM pockel cell gain, float point value: 0.0 ~ 1.0
lsm-pmt-gain : 0.4
# LSM PMT gain, float point value: 0.0 ~ 1.0
slide-box : [-100, 600, 25500.0, 17000.0]
# Pre-define scan area (read out values from the stage):
# (start x stage position, start y stage position, end x stage position, end y stage position)
lsm-enhancer : null
bf-enhancer : null
classifier : null
model_config:
adv-interval: 3
average-factor: 50
batch-size: 8
blindspot-rate: 0.05
cnn-base-channel: 8
dataset: datasets/PA_2081b
gan-lambda: 5
gpu: true
image-channel: 1
image-extension: tif
iter-per-epoch: 200
iterations: 200000
learning-rate: 0.0001
load-weights: supervised2022-08-07_13-02-52
loss-gain: 1000
norm-range:
- 5420
- 44017
norm-range-target:
- 6265
- 38567
only-pixel-loss: false
percep-lambda: 0.5
resolution: 512
test-interval: 5
threads: 0
up-scale-factor: 2
hard_config:
pixel-size-bf-20x : 0.222 # 0.222 micron/pixel at (1392, 1040)
pixel-size-bf-4x : 1.105 # 1.305 micron/pixel at (1392, 1040)
pixel-size-shg-base : 0.509 # 0.509 micron/pixel at 256
pixel-size-shg : 0.509
camera-resolution : [1392, 1040] # (width, height)
lsm-resolution-base : [512, 512]
slide-size : [40000.0, 20000.0] # (width, height) (70000, -20000)
Z-stage-20x : -6980 # -6930 + 290 / 10500
Z-stage-laser : -6640 #-6640
Z-stage-4x : 3570 # -2300
F-stage-20x : -15800 # 11000
F-stage-laser : -18500 # -17500
F-stage-4x : -1000
Z-bf-offset : -10560
Z-laser-offset : 290
hard-limit-z : [-8500.0, 17000.0]
hard-limit-x : [-5000.0, 40000.0]
hard-limit-y : [-4200, 25000.0] #(-2200, 19000.0)
hard-limit-f : [-19000, 0]
20x-bf-offset : [-600, 10] # 4x + this value to 20x // (-590, 74)
shg-offset : [-580, -280] # 4x + this value to shg // (-580, -172)
led-4x : 4
led-20x : 5
focus-device : 'ZStage:Z:32'
condensor-device : 'ZStage:F:32'
led-device : ['LED-Dev1ao0', 'Voltage']
obj-device : ['Turret:O:35', 'Label']