xstage

Illumina HiSeq 2500 Systems :: X-STAGE

Uses command set from Schneider Electric MCode

The xstage can be moved from step positions 1000 to 50000. Initially, the xstage is homed to step position 30000. Lower step positions are to the right, and higher step positions are to the left. Each xstage step is 0.375 microns.

Example:

#Create xstage
import pyseq
xstage = pyseq.xstage.Xstage('COM9')
#Initialize xstage
xstage.initialize()
#Move xstage to step position 10000
xstage.move(10000)
10000
TODO:

  • Change initialization to be aware position of flags.

Classes

Xstage(com_port[, baudrate, logger])

Illumina HiSeq 2500 Systems :: X-STAGE
class pyseq.xstage.Xstage(com_port, baudrate=9600, logger=None)

Illumina HiSeq 2500 Systems :: X-STAGE

Attributes:

  • spum (float): Number of xstage steps per micron.

  • position (int): The absolution position of the xstage in steps.

  • min_x (int): Minimum safe xstage step position.

  • max_x (int): Maximum safe xstage step position.

  • home (int): Step position to move xstage out.

check_home()

Return True if in correct home position.

check_position(position)

Check if xstage is in position.

Parameters:

  • position (int): Absolute step position must be between 1000 - 50000.

Returns:

  • bool: True if xstage is in position, False if it is not in position.

command(text)

Send a serial command to the xstage and return the response.

Parameters:

  • text (str): A command to send to the xstage.

Returns:

  • str: The response from the xstage.

initialize()

Initialize the xstage.

move(position)

Move xstage to absolute step position.

Parameters:

  • position (int): Absolute step position must be between 1000 - 50000.

Returns:

  • int: Absolute step position after move.