zstage

Illumina HiSeq 2500 System :: Z-STAGE

Uses commands found on hackteria

The zstage can be moved up and down by 3 independent tilt motors. Each tilt motor can from step positions 0 to 25000. Initially, all of the tilt motors in the zstage are homed to step position 0. Lower step positions are down, and higher step positions are up. Each tilt motor step is about 1.5 microns. These motors are not precise and not repeatable. That is they are not expected to go to the exact step position and they are not expected to go to the same position over and over again.

Example:

#Create zstage
import pyseq
zstage = pyseq.zstage.Zstage('COM10')
#Initialize zstage
zstage.initialize()
#Move all tilt motors on zstage to absolute step position 21000
zstage.move([21000, 21000, 21000])
[21000, 21000, 21000]

Classes

Zstage(fpga[, logger])

Illumina HiSeq 2500 System :: Z-STAGE
class pyseq.zstage.Zstage(fpga, logger=None)

Illumina HiSeq 2500 System :: Z-STAGE

Attributes:

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

  • position ([int, int, int]): A list with absolute positions of each tilt motor in steps.

  • motors ([int, int, int]): Motor ids.

  • tolerance (int): Maximum step error allowed, default is 2.

  • min_z (int): Minimum zstage step position.

  • max_z (int): Maximum safe zstage step position.

  • xstep ([int, int, int]): Xstage position of the respective motors.

  • ystep ([int, int, int]): Ystage position of the respective motors.

  • image_step (int): Initial step position of motors for imaging

  • logger (logger): Logger for messaging.

  • focus_pos (int): Step used used for imaging.

  • active (bool): Flag to enable/disable z stage movements.

check_position()

Return a list with absolute positions of each tilt motor.

Returns:

  • [int, int ,int]: List of absolution positions.

command(text)

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

Parameters:

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

Returns:

  • str: The response from the zstage.

get_motor_points()

Return stage step coordinates tilt motors.

in_position(position)

Return True if all motors are in position, False if not.

Parameters:

  • position ([int,int,int]): List of motor positions to test.

Returns:

  • bool: True if all motors are in position, False if not.

initialize()

Initialize the zstage.

move(position)

Move all tilt motors to specified absolute step positions.

Parameters:

  • position ([int, int, int]): List of absolute positions for each tilt motor.

Returns:

  • [int, int, int]: List with absolute positions of each tilt motor after the move.