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TEM Controller options

Added by Trishant Umrekar over 2 years ago

Hi,

Our EFGlacios is fitted with a Selectris energy filter and I am unsure of how to control slit width and insertion (preferably in presets?).

In addition to this, the TEM Controller node does not communicate with the apertures or grid loader (No state change when changing aperture or grid). Pressure values and column valve communication are active.

Which scripts should I be interacting with to implement these?

Best regards,
Trishant


Replies (5)

TEM Controller options - Added by Wim Hagen over 2 years ago

Apertures are only accessible with some special scripting option that nobody has ever been able to obtain. Could be that the loader stuff has moved to advanced scripting due to software upgrades needed for Selectris.
Best,
Wim

On 7. Mar 2022, at 16:53, wrote:


Leginon - Leginon: TEM Controller options
Trishant Umrekar
Hi,

Our EFGlacios is fitted with a Selectris energy filter and I am unsure of how to control slit width and insertion (preferably in presets?).

In addition to this, the TEM Controller node does not communicate with the apertures or grid loader (No state change when changing aperture or grid). Pressure values and column valve communication are active.

Which scripts should I be interacting with to implement these?

Best regards,
Trishant

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RE: TEM Controller options - Added by Anchi Cheng over 2 years ago

Selectris control is through Advanced Scripting. If you search the computer, you may find "Advanced TEM Scriptin User Guide.pdf". Even if you have not done instrument control before, you can read my pyscope/feicam.py code where I do basic Camera Acquisition on how to hold on to a COM object pointer and set Attributes. You will be looking for EnergeFilter object and want to set Insert/Retract and Width.

I am not sure if AutoLoader interface in Advanced Scripting replaces the old TEMScripting one or just as alternative. The one I have in Leginon uses the old one which is always available, too. since magnification and all other TEM optic controls are there. I don't expect they disable anything in there.

You can check with python command line to see if pyscope (leginon's instrument interface subpackage) can access it.

from pyscope import fei
f=fei.EFGlacios()
f.hasGridLoader()         #This should return True
f.getGridLoaderSlotState(1)        #This should return something other than 'unknown'

If you get False in f.hasGridLoader(), you may want to make it raise the exception so we know what it says.

f.tecnai.AutoLoader.AutoLoaderAvailable

For aperture control, since I could not convince TFS to let us insert/retract through scripting, I wrote AutoIt scripts to do so. They are similar to Wim's phase plate "next" script. See Aperture_selection_through_tem_controller It takes a bit of customization since button ids are not the same on all interfaces. If you can not understand how to customize it, post here your TUI Aperture panel screenshot. I can then tell you what to set.

TEM Controller options - Added by Bridget Carragher over 2 years ago

Should we try again to push TFS into giving us this access?
B

On Mar 7, 2022, at 11:01 AM, Wim Hagen <<mailto:>> wrote:

Apertures are only accessible with some special scripting option that nobody has ever been able to obtain. Could be that the loader stuff has moved to advanced scripting due to software upgrades needed for Selectris.
Best,
Wim

On 7. Mar 2022, at 16:53, <mailto:> wrote:


Leginon - Leginon: TEM Controller options<https://emg.nysbc.org/boards/6/topics/3599>
Trishant Umrekar

Hi,

Our EFGlacios is fitted with a Selectris energy filter and I am unsure of how to control slit width and insertion (preferably in presets?).

In addition to this, the TEM Controller node does not communicate with the apertures or grid loader (No state change when changing aperture or grid). Pressure values and column valve communication are active.

Which scripts should I be interacting with to implement these?

Best regards,
Trishant

You have received this notification because you have either subscribed to it, or are involved in it.
To change your notification preferences, please click here: http://emg.nysbc.org/my/account

--------------------------------------------------------------------------
Bridget Carragher
Simons Electron Microscopy Center (semc.nysbc.org<http://semc.nysbc.org&gt;)
National Resource for Automated Molecular Microscopy
National Center For CryoEM Access and Training
National Center for In-situ Tomographic Ultramicroscopy
New York Structural Biology Center
89 Convent Avenue, New York NY 10027
(212) 939-0660; <mailto:>
--------------------------------------------------------------------------

TEM Controller options - Added by Anchi Cheng over 2 years ago

It would be nice to have, but workaround does work.

Anchi

On Mar 8, 2022, at 5:25 PM, Bridget Carragher <<mailto:>> wrote:

Should we try again to push TFS into giving us this access?
B

On Mar 7, 2022, at 11:01 AM, Wim Hagen <<mailto:>> wrote:

Apertures are only accessible with some special scripting option that nobody has ever been able to obtain. Could be that the loader stuff has moved to advanced scripting due to software upgrades needed for Selectris.
Best,
Wim

On 7. Mar 2022, at 16:53, <mailto:> wrote:


Leginon - Leginon: TEM Controller options<https://emg.nysbc.org/boards/6/topics/3599>
Trishant Umrekar

Hi,

Our EFGlacios is fitted with a Selectris energy filter and I am unsure of how to control slit width and insertion (preferably in presets?).

In addition to this, the TEM Controller node does not communicate with the apertures or grid loader (No state change when changing aperture or grid). Pressure values and column valve communication are active.

Which scripts should I be interacting with to implement these?

Best regards,
Trishant

You have received this notification because you have either subscribed to it, or are involved in it.
To change your notification preferences, please click here: http://emg.nysbc.org/my/account

--------------------------------------------------------------------------
Bridget Carragher
Simons Electron Microscopy Center (semc.nysbc.org<http://semc.nysbc.org/&gt;)
National Resource for Automated Molecular Microscopy
National Center For CryoEM Access and Training
National Center for In-situ Tomographic Ultramicroscopy
New York Structural Biology Center
89 Convent Avenue, New York NY 10027
(212) 939-0660; <mailto:>
--------------------------------------------------------------------------

RE: TEM Controller options - Added by Trishant Umrekar over 2 years ago

Anchi Cheng wrote:

Selectris control is through Advanced Scripting. If you search the computer, you may find "Advanced TEM Scriptin User Guide.pdf". Even if you have not done instrument control before, you can read my pyscope/feicam.py code where I do basic Camera Acquisition on how to hold on to a COM object pointer and set Attributes. You will be looking for EnergeFilter object and want to set Insert/Retract and Width.

I am not sure if AutoLoader interface in Advanced Scripting replaces the old TEMScripting one or just as alternative. The one I have in Leginon uses the old one which is always available, too. since magnification and all other TEM optic controls are there. I don't expect they disable anything in there.

You can check with python command line to see if pyscope (leginon's instrument interface subpackage) can access it.

[...]

If you get False in f.hasGridLoader(), you may want to make it raise the exception so we know what it says.
[...]

For aperture control, since I could not convince TFS to let us insert/retract through scripting, I wrote AutoIt scripts to do so. They are similar to Wim's phase plate "next" script. See Aperture_selection_through_tem_controller It takes a bit of customization since button ids are not the same on all interfaces. If you can not understand how to customize it, post here your TUI Aperture panel screenshot. I can then tell you what to set.

Trying the script to check for Autloader communication seems to work and produces the following:

>>> from pyscope import fei
>>> f=fei.EFGlacios()
>>> f.hasGridLoader()
True
>>> f.getGridLoaderSlotState(1)
'empty'
>>> f.getGridLoaderSlotState(8)
'occupied'
>>> f.getGridLoaderNumberOfSlots()
12

And this is mirrored by the display in TEMController now (I don't know what changed). I can freely swap grids in and out using Scope_Control now, too.
The aperture states are still "unknown", of course. It seems that there is objective aperture control for phase plate position cycling, but no more than that.

I will use feicam.py and the information in the advanced tem scripting user guide to make a connection with the Selectris. Hope to update you soon.

Thanks.

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