Leginon

Something to be aware of:
As of TFS temserver SW version 7.9.0 (so 3.9.0 for Krios and 2.9.0 for Talos/Glacios), the EFTEM lens series (used for energy filters) has changed, but only for Selectris energy filters. If TFS install a Selectris, ask for that software version since all EFTEM magnifications and image rotations change slightly, this way one has to calibrate things only once. We have been running 2.9.0 on our Glacios/Selectris Falcon 4 for six weeks now without trouble,

@Anchi Cheng, in SerialEM we then run into an unforeseen problem that the mag index of the lowest M/SA mode is not the same anymore for TEM and EFTEM mode….

Best,

Wim Hagen
EMBL Heidelberg

On 13. Sep 2021, at 11:58, semcit@nysbc.org wrote:

Leginon - Leginon: Progress on Selectris support? <https://emg.nysbc.org/boards/6/topics/3559&gt;Morgan Beeby
Hi Anchi,

Our Selectris is due to be installed on our Glacios + Falcon IV next week (exciting).

I wondered how Selectris support is going with Leginon?

thanks,

Morgan

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 <http://emg.nysbc.org/my/account>

Thanks, Wim, this is very useful. I will be in touch with TFS now to make sure this happens.

Morgan

Thank Wim!
Best regards,
Bridget

On Sep 13, 2021, at 6:24 AM, Wim Hagen <hagen@embl.de<mailto:hagen@embl.de>> wrote:

Something to be aware of:
As of TFS temserver SW version 7.9.0 (so 3.9.0 for Krios and 2.9.0 for Talos/Glacios), the EFTEM lens series (used for energy filters) has changed, but only for Selectris energy filters. If TFS install a Selectris, ask for that software version since all EFTEM magnifications and image rotations change slightly, this way one has to calibrate things only once. We have been running 2.9.0 on our Glacios/Selectris Falcon 4 for six weeks now without trouble,

@Anchi Cheng, in SerialEM we then run into an unforeseen problem that the mag index of the lowest M/SA mode is not the same anymore for TEM and EFTEM mode….

Best,

Wim Hagen
EMBL Heidelberg

On 13. Sep 2021, at 11:58, semcit@nysbc.org<mailto:semcit@nysbc.org> wrote:

Leginon - Leginon: Progress on Selectris support?<https://emg.nysbc.org/boards/6/topics/3559>
Morgan Beeby

Hi Anchi,

Our Selectris is due to be installed on our Glacios + Falcon IV next week (exciting).

I wondered how Selectris support is going with Leginon?

thanks,

Morgan

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; bcarr@nysbc.org<mailto:bcarr@nysbc.org>
--------------------------------------------------------------------------

Thanks, Wim, for the tip.

Morgan, I have the software version and the doc to start this with. The energy filter is supposed to be stable over time, so we will start with the minimal, i,e, not to align the slit. TFS only gave the low-level command to move the slit, not a call to perform the whole slit alignment automatically from scripting, so I will have to work on the actual alignment algorithm when I have one to try on. Ours are not yet scheduled to install. I might have to send some scripts for you to test.

Anchi,

Excellent. Yes, I think a simple slit in/out checkbox is, pragmatically, all we will need. Alignments can probably be safely left to TFS software.

I'll let you know when we've got it installed and I have a Leginon client running.

thanks,

Morgan

Anchi,

Our Glacios + Selectris + Falcon4EC were handed over to us today to configure Leginon.

We wondered what the bare basic modifications we'll need to make to get things working?

My guess is that we need to add an EFGlacios class to pyscope/fei.py that would look like this?

class EFGlacios(Glacios):
        name = 'EF-Glacios'
        column_type = 'talos'
        use_normalization = True
        projection_lens_program = 'EFTEM'

Looking over K2/K3 config, it doesn't seem that we need to make any alterations to the Falcon4EC, as the EFGlacios will take into account lens changes? Is there anything else we'll need to consider?

Morgan

(We tried this EFGlacios class and it didn't work -- it couldn't pick up the mag tables)

Sorry for not seeing this earlied. I worked on this before GRC. We will have to put selectrus control in the module that uses advances TEM Scripting. That comlicates things a bit but still solvable. I am surprised that EFGlacios you made could not pick up the mag tables, though. That part should work. I will ask TFS about it.

Keep in mind the EFTEM lens series for Selectris systems is software version dependent, maybe that causes trouble?
Best,
Wim

On 17. Nov 2021, at 18:21, semcit@nysbc.org wrote:


Leginon - Leginon: RE: Progress on Selectris support?
Anchi Cheng
Sorry for not seeing theI worked on this before GRC. We will have to put selectrus control in the module that uses advances TEM Scripting. That comlicates things a bit but still solvable. I am surprised that EFGlacios you made could not pick up the mag tables, though. That part should work. I will ask TFS about it.

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

Morgan, can you post your specific software version ?

Hi Anchi,

We're on TEMServer 7.9.1.

FYI this is the PyScope error we get when we add the EFGlacios class:

C:\Python27>python
Python 2.7.3 (default, Apr 10 2012, 23:31:26) [MSC v.1500 32 bit (Intel)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> from pyscope import fei
>>> scope = fei.EFGlacios()
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:\Python27\lib\site-packages\pyscope\fei.py", line 89, in __init__
    self.tom = comtypes.client.CreateObject('TEM.Instrument.1')
  File "C:\Python27\lib\site-packages\comtypes\client\__init__.py", line 224, in CreateObject
    clsid = comtypes.GUID.from_progid(progid)
  File "C:\Python27\lib\site-packages\comtypes\GUID.py", line 78, in from_progid
    _CLSIDFromProgID(unicode(progid), byref(inst))
  File "_ctypes/callproc.c", line 936, in GetResult
WindowsError: [Error -2147221005] Invalid class string
>>>

(i.e., we don't even get as far as trying to retrieve mag tables).

Let me know if there's anything else I can send you from our end.

thanks,

Morgan

I fixed that in September. If you are on myami-beta or trunk branch, please do a pull.

Excellent, Anchi -- that worked. Thank you.