[3dem] K3 CDS mode issue

Thu Dec 23 21:39:18 PST 2021

I should note that the TFS keeps the newest GMS version, but only the 
firmware was reverted to the old version. In this settings, "first frame 
noise issue" is not solved.

Best,

Tomohiro

On 2021/12/24 13:41, Tomohiro Nishizawa wrote:
> Dear list,
>
> We actually updated to the newer version pf GMS (probably newer than 
> 3.44.3420), but it turned that the updated firmware damages the K3 
> processor and finally reverted to the old version. So we are awaiting 
> TFS to solve this problem. As far as I know, three Krios in Japan are 
> in the same situation.
>
> Best,
>
> Tomohiro
>
>
>
> On 2021/12/24 3:04, Wim Hagen wrote:
>> ■[YCU Notice] 送信履歴のない送信元です。URL接続要注意。■
>>
>>
>> Dear Nadav,
>>
>> We run GMS 3.44.3420 (with some patches) on Krios G3i Bioquantum K3, 
>> it works with TFS EPU and Tomo (temserver versions >=3.8) and I 
>> reported this some time ago to TFS. As you have Gatan integration, 
>> you obviously purchased all things from TFS, so TFS are responsible 
>> for proper system operation. Gatan has a solution for their part, but 
>> TFS will not test, release and support that solution: that’s pretty 
>> sad to hear.
>>
>> Best,
>>
>> Wim
>>
>>> On 23. Dec 2021, at 08:57, Nadav Elad <nadav.elad at weizmann.ac.il> 
>>> wrote:
>>>
>>> Dear list
>>>
>>> I would like to continue the CDS discussion. Tomohiro mentioned 
>>> below that the first CDS frame contains heavy noise. We see that as 
>>> well using GMS version 3.32. Gatan are saying that the bug is solved 
>>> in all builds of GMS newer than 3.43, so they recommend upgrading. 
>>> However, we have the K3 embedded in the Thermo software, and they 
>>> are refusing to support this GMS version, saying that it causes loss 
>>> of the K3 in EPU and other software. We do not want to disrupt EPU 
>>> functionality as many of our users prefer it.
>>>
>>> Does anyone have experience with this bug being solved in GMS 3.43?
>>> And, is anyone running this GMS version or newer together with 
>>> Thermo software?
>>>
>>> Thank you,
>>> Best wishes
>>> Nadav
>>>
>>>
>>> -- 
>>> Nadav Elad, Ph.D.
>>> Electron Microscopy Unit
>>> Weizmann Institute of Science
>>> Rehovot, Israel
>>> Tel: +972 (0) 8 934 2115
>>> Mobile:  +972 (0) 52 3909 420
>>> Email:  nadav.elad at weizmann.ac.il
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>>>
>>>
>>>
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>>> CDS movies contain heavy noises on the first frame. This problem has 
>>> not
>>> been solved even after very recent updates in some Krios in Japan. But
>>> the attached images imply wrong gain-correction.
>>>
>>> Have you checked that the path to the gain reference file is correct?
>>> After recent update on GMS, the file name of the gain-reference was
>>> slightly changed. If you are using SerialEM, you have to update the 
>>> path
>>> to the gain-reference, or you can simply make a symbolic link to the
>>> correct gain file.
>>>
>>> Did you ever try making gain-file from the data (by using
>>> relion_estimate_gain)?
>>> If it works, internal setting for the gain reference is somewhat wrong.
>>>
>>> Best,
>>>
>>> Tomohiro
>>>
>>>
>>>> On 2021/12/18 4:07, Matthijn VOS wrote:
>>>>
>>>> Exactly the same experience at Institut Pasteur. Took more than a
>>>> year, then GMS upgrade, gatan engineer playing with the settings and
>>>> gain recorded not at the dose rate requested by the procedure, but a
>>>> bit higher.
>>>>
>>>> No explanations from gatan as were the origin of this all comes from.
>>>> To this day not very satisfied and working on replacing it with a TF
>>>> filter and camera.
>>>>
>>>> Happy holidays!
>>>>
>>>>>> On Dec 17, 2021, at 13:06, Wim Hagen <hagen at embl.de> wrote:
>>>>> 
>>>>>
>>>>> Hi Dan,
>>>>>
>>>>> Our K3 has/had this exact problem from the very start when it was
>>>>> installed. For SPA one can somewhat work around the problem, but it’s
>>>>> a killer for tomography. Gatan played a bit with the detection
>>>>> settings for CDS mode (which required a GMS upgrade), that somewhat
>>>>> fixed the gain ref symptoms, but a subsequent ApoF SPA test of normal
>>>>> vs CDS mode showed zero difference in performance. We kinda left it
>>>>> there and only use normal mode on that system.
>>>>>
>>>>> Hearsay:
>>>>> - Some systems have this in normal mode, or CDS mode or both modes.
>>>>> -Some systems were fine after swapping the chip.
>>>>> - One system was fine after swapping the K3 power supply.
>>>>>
>>>>> Best,
>>>>>
>>>>> Wim Hagen
>>>>> EMBL Heidelberg
>>>>>
>>>>>
>>>>>> On 17. Dec 2021, at 02:44, Daniel Toso <dtoso at berkeley.edu> 
>>>>>> wrote:
>>>>>> 
>>>>>> Hello Everyone,
>>>>>>
>>>>>> We have been having an issue with one of our older K3 cameras since
>>>>> last year. Namely, in CDS mode we are getting stripes in our images
>>>>> that do not get removed by gain correction and become worse as the
>>>>> dose goes further from 7.5 e-/pixel/sec., which will occur quite
>>>>> often in thicker ice. See attached image for an example.
>>>>>> We tried having Gatan (Ametek) fix the issue but they do not have a
>>>>> solution beyond buying a new sensor.
>>>>>> I was wondering if this is a widespread issue. Also, if there is
>>>>> any solution besides no longer imaging in CDS mode. We have heard
>>>>> that it is also seen at UCSF. Any advice would be appreciated.
>>>>>> Thanks very much!
>>>>>>
>>>>>> Best regards,
>>>>>>
>>>>>> Dan
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