Zeiss macro to start FCS measurements along Z axis?

Software
1

Dear community,

On a Zeiss LSM 980, we’re trying to start FCS measurements along multiple points on the Z axis. The FCS measurement itself runs fine. We thought we’d first set the ideal z position to zero, then start macro recording where we

  1. move the z position (e.g. 10 microns)
  2. measure FCS
    and repeat these two steps (ideally set as a loop but not absolutely necessary).

The issues we’re having:

  1. Any change in z position (e.g. an increment of 1.0 microns in the “focus” tab) records both absolute and relative numbers in the macro
  2. when removing the absolute numbers but retaining the relative ones, the focus moves accordingly in z (as judged on the touchscreen panel) and stays there for a second or so, but then moves back to the original position to run the measurement.

The scope is an upright 980 and software is Zen Blue (I think 3.10; the macro records as Zen26).

A sample macro text is below but as said it repeats the measurement at z=0.
Ideally it would also fit the FCS data and possibly export the data automatically, but those are future problems.

If I may, I’m tagging @sebi06 here :slight_smile:

hardwaresetting1 = ZenHardwareSetting()
hardwaresetting1.SetParameter('MTBLKM980Laser561', 'IsEnabled', 'true')
Zen.Devices.ApplyHardwareSetting(hardwaresetting1)

hardwaresetting1.SetParameter('MTBLSM880DetectorMeta', 'DetectorGain', '1045')
Zen.Devices.ApplyHardwareSetting(hardwaresetting1)
hardwaresetting1.SetParameter('MTBLSM880DetectorLong', 'DetectorGain', '990')
Zen.Devices.ApplyHardwareSetting(hardwaresetting1)
experiment1 = Zen.Acquisition.Experiments.GetByName("fcs.czexp")

# CAUTION! Risk of Crushing when executing code!
Zen.Devices.Focus.TargetPosition = 10.0
Zen.Devices.Focus.Apply()
fcsimage1 = Zen.Acquisition.AcquireImage(experiment1)

# CAUTION! Risk of Crushing when executing code!
Zen.Devices.Focus.TargetPosition = 9.0
Zen.Devices.Focus.Apply()
fcsimage2 = Zen.Acquisition.AcquireImage(experiment1)


# CAUTION! Risk of Crushing when executing code!
Zen.Devices.Focus.TargetPosition = 8.0
Zen.Devices.Focus.Apply()
fcsimage3 = Zen.Acquisition.AcquireImage(experiment1)


# CAUTION! Risk of Crushing when executing code!
Zen.Devices.Focus.TargetPosition = 7.0
Zen.Devices.Focus.Apply()
fcsimage4 = Zen.Acquisition.AcquireImage(experiment1)


# CAUTION! Risk of Crushing when executing code!
Zen.Devices.Focus.TargetPosition = 6.0
Zen.Devices.Focus.Apply()
fcsimage5 = Zen.Acquisition.AcquireImage(experiment1)


# CAUTION! Risk of Crushing when executing code!
Zen.Devices.Focus.TargetPosition = 5.0
Zen.Devices.Focus.Apply()
fcsimage6 = Zen.Acquisition.AcquireImage(experiment1)


# CAUTION! Risk of Crushing when executing code!
Zen.Devices.Focus.TargetPosition = 4.0
Zen.Devices.Focus.Apply()
fcsimage7 = Zen.Acquisition.AcquireImage(experiment1)


# CAUTION! Risk of Crushing when executing code!
Zen.Devices.Focus.TargetPosition = 3.0
Zen.Devices.Focus.Apply()
fcsimage8 = Zen.Acquisition.AcquireImage(experiment1)


# CAUTION! Risk of Crushing when executing code!
Zen.Devices.Focus.TargetPosition = 2.0
Zen.Devices.Focus.Apply()
fcsimage9 = Zen.Acquisition.AcquireImage(experiment1)

# CAUTION! Risk of Crushing when executing code!
Zen.Devices.Focus.TargetPosition = 1.0
Zen.Devices.Focus.Apply()
fcsimage10 = Zen.Acquisition.AcquireImage(experiment1)

# CAUTION! Risk of Crushing when executing code!
Zen.Devices.Focus.TargetPosition = 0.0
Zen.Devices.Focus.Apply()
fcsimage11 = Zen.Acquisition.AcquireImage(experiment1)

# CAUTION! Risk of Crushing when executing code!
Zen.Devices.Focus.TargetPosition = -1.0
Zen.Devices.Focus.Apply()
fcsimage12 = Zen.Acquisition.AcquireImage(experiment1)


# CAUTION! Risk of Crushing when executing code!
Zen.Devices.Focus.TargetPosition = -2.0
Zen.Devices.Focus.Apply()
fcsimage13 = Zen.Acquisition.AcquireImage(experiment1)


# CAUTION! Risk of Crushing when executing code!
Zen.Devices.Focus.TargetPosition = -3.0
Zen.Devices.Focus.Apply()
fcsimage14 = Zen.Acquisition.AcquireImage(experiment1)


# CAUTION! Risk of Crushing when executing code!
Zen.Devices.Focus.TargetPosition = -4.0
Zen.Devices.Focus.Apply()
fcsimage15 = Zen.Acquisition.AcquireImage(experiment1)


# CAUTION! Risk of Crushing when executing code!
Zen.Devices.Focus.TargetPosition = -5.0
Zen.Devices.Focus.Apply()
fcsimage16 = Zen.Acquisition.AcquireImage(experiment1)


# CAUTION! Risk of Crushing when executing code!
Zen.Devices.Focus.TargetPosition = -6.0
Zen.Devices.Focus.Apply()
fcsimage17 = Zen.Acquisition.AcquireImage(experiment1)


# CAUTION! Risk of Crushing when executing code!
Zen.Devices.Focus.TargetPosition = -7.0
Zen.Devices.Focus.Apply()
fcsimage18 = Zen.Acquisition.AcquireImage(experiment1)


# CAUTION! Risk of Crushing when executing code!
Zen.Devices.Focus.TargetPosition = -8.0
Zen.Devices.Focus.Apply()
fcsimage19 = Zen.Acquisition.AcquireImage(experiment1)

# CAUTION! Risk of Crushing when executing code!
Zen.Devices.Focus.TargetPosition = -9.0
Zen.Devices.Focus.Apply()
fcsimage20 = Zen.Acquisition.AcquireImage(experiment1)

# CAUTION! Risk of Crushing when executing code!
Zen.Devices.Focus.TargetPosition = -10.0
Zen.Devices.Focus.Apply()
fcsimage21 = Zen.Acquisition.AcquireImage(experiment1)
2

For anyone else running into issues with macros on their Zeiss confocal microscopes I’ll answer my own question: One way to move forward on some macro tasks can be to use a mouse (and possibly keyboard key stroke) position & click recorder. This can possibly be encoded once you’re aware that macros run on IronPython (a mix of python 2 and Microsoft .NET), or get in contact with Zeiss directly.
Happy imaging!