optics¶

Illumina HiSeq 2500 System :: Optics

Uses commands found on hackteria

Controls the excitation and emission filters on the Illumina HiSeq 2500 System. The excitation filters are optical density filters that block a portion of the light to quickly change between laser intensities. The percent of light passed through is 10**-OD*100 where OD is the optical density of the filter. All of the light is blocked, laser intensity = 0 mW at the home “filter”. None of the light is blocked, laser intensity = the set power of the laser, at the open “filter”. The names and OD of available filters are listed in the following table.

laser color

laser index

filters (Optical Density)

green

1

open, 1.0, 2.0, 3.5, 3.8, 4.0, 4.5, home

red

2

open, 0.2, 0.5, 0.6, 1.0, 2.4, 4.0, home

The emission filter has 2 states, in the light path or out of the light path.

Examples:

#Create optics object
import pyseq
fpga = pyseq.fpga.FPGA('COM12','COM15')
fpga.initialize()
optics = pyseq.optics.Optics(fpga)
#Initialize optics
optics.initialize()
# Move to green line OD1.6 filter and red line OD1.0 filter
optics.move_ex('green','1.6')
optics.move_ex('red','1.0')
# Move the emission filter out of the light path
optics.move_em_in(False)

Classes

Optics(fpga[, logger, colors])

Illumina HiSeq 2500 System :: Optics

class pyseq.optics.Optics(fpga, logger=None, colors=['green', 'red'])¶

Illumina HiSeq 2500 System :: Optics

Attributes:

ex ([str,str]): The current excitation filter for each laser line. The first filter is for the green laser and the second filter for the red laser.
em_in (bool): True if the emission filter is in the light path or False if the emission filter is out of the light path.
colors (dict): Laser dictionary of color keys and index values.
cycle_dict[dict,dict]: Dictionaries of filters to use for each laser line at different cycles. The first dictionary is for the green laser and the second dictionary is for the red laser.
focus_filters (list): Filter to use for each laser line during autofocus.

command(text)¶

Send a command to the optics and return the response.

Parameters: text (str): A command to send to the optics.

Returns: str: The response from the optics.

initialize()¶

Initialize the optics.

The default position for the excitation filters is home which blocks excitation light. The default position for the emission filter is in the light path.

move_em_in(INorOUT)¶

Move the emission filter in to or out of the light path.

Parameters:

INorOUT (bool): True for the emission in the light path or False for the emission filter out of the light path.

move_ex(color, position)¶

Move the excitation wheel to the specified position.

The excitation filters are optical density filters that block a portion of the light to quickly change between laser intensities. The percent of light passed through is 10**-OD*100 where OD is the optical density of the filter. All of the light is blocked with the home “filter”. The names and OD of available filters are listed in the following table.

laser color	laser index	filters
green	1	open, 0.2, 0.6, 1.4, 1.6, 2.0, 4.0, home
red	2	open, 0.2, 0.9, 1.0, 2.0, 3.0, 4.5, home

Parameters:

color (str): The color of laser line.
position (str): The name of the filter to change to.