#Create HiSeq object
import pyseq
hs = pyseq.HiSeq()
#Initialize cameras
hs.initializeCams()
#Initialize Instruments, will take a few minutes
hs.initializeInstruments()
#Specify directory to save images in
hs.image_path = 'C:\\Users\\Public\\HiSeqImages\\'
#Get stage positioning and imaging details for section on flowcell A
pos = hs.position('A', [15.5, 45, 10.5, 35])
#Set laser intensities to 200 mW
hs.lasers['green'].set_power(200)
hs.lasers['red'].set_power(200)
#Move to center of section
hs.x.move(pos['x_center'])
12000
hs.y.move(pos['y_center'])
True
#Move stage to imaging position.
hs.z.move([21500, 21500, 21500])
#Move excitation filters to optical density 1.0
hs.optics.move_ex('green', 1.0)
hs.optics.move_ex('red', 1.0)
#Find focus
hs.autofocus(pos)
True
# Take a 32 frame picture, creates image for each channel 2048 x 4096 px
hs.take_picture(32, image_name='FirstHiSeqImage')
#Move stage to the initial image scan position and scan image at 1 obj plane
hs.x.move(pos['x_initial'])
10000
hs.y.move(pos['y_initial'])
True
#Move excitation filters to open position
hs.optics.move_ex('green', 'open')
hs.optics.move_ex('red', 'open')
hs.scan(pos['n_scans'], 1, pos['n_frames'], image_name='FirstHiSeqScan')