[3view] 3view Digest, Vol 4, Issue 3

Jörgen Kornfeld Joergen.Kornfeld at mpimf-heidelberg.mpg.de
Wed Oct 8 16:43:02 CEST 2014


Am 08.10.2014 13:27, schrieb saskial:
> Hi everyone,
>
> thank you very much for your replies.
> We will have to keep an eye on it, to see if this comes back regularly.
> @ Jurgen: In case of the cutter piezo was broken, did this occur every
> time? When we stop the approach and start again, it usually disappears
> and then it doesn't happen any more for a couple of runs.
Not every time, but we replaced it as soon as we saw it. I would guess 
that the frequency of these stutterings increases over time. You could 
just monitor it and see whether it becomes worse (maybe weeks or 
months), but I would also assume that the stack acquisition is affected 
by it, especially for cuts below 30 nm thickness. Also my guess is that 
it happens more often for thicker cuts due to the increased cutting 
forces. You could try 200 nm cuts and then see whether it happens more 
often than with 25 nm. However, I do not have a good inituition about 
the strength of the cutting forces relative to some internal friction 
that might cause this, so this might make no difference. Good luck!

-Jörgen


>
> Kind regards,
>
> Saskia
>
>
>
>
> On 2014-10-08 12:00, 3view-request at open-em.org wrote:
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>> Today's Topics:
>>
>>    1. Re: 3view Digest, Vol 4, Issue 2 (Beckett, Alison)
>>
>> List-Post: <mailto:3view at open-em.org>
>> Content-Transfer-Encoding: quoted-printable
>> From: "Beckett, Alison" <A.J.Beckett at liverpool.ac.uk>
>> Precedence: list
>> MIME-Version: 1.0
>> To: "3view at open-em.org" <3view at open-em.org>
>> References: <mailman.3.1412710947.2520.3view at open-em.org>
>> In-Reply-To: <mailman.3.1412710947.2520.3view at open-em.org>
>> Date: Tue, 7 Oct 2014 21:05:59 +0000
>> Reply-To: Mailing list for Gatan 3View Serial Block-Facing
>> <3view at open-em.org>
>> Message-ID:
>> <E2CDDE082CC00249B7C8C235A1EB098F965FA59E at BHEXMBX1.livad.liv.ac.uk>
>> Content-Type: text/plain; charset="us-ascii"
>> Subject: Re: [3view] 3view Digest, Vol 4, Issue 2
>> Message: 1
>>
>> Hi Saskia,
>>
>> We had an issue last week. The knife was going through its full
>> clearing pr=
>> ocedure with every cut. Then, after I had stopped the cutting cycle,
>> it sta=
>> rted cutting on its own, twice!
>>
>> Rebooting the computer seems to have fixed the problem.
>>
>> Cheers,
>>
>> Ali
>>
>> Alison J. Beckett
>> Biomedical Electron Microscopy Unit
>> University of Liverpool
>> Liverpool
>> L69 3BX
>> http://www.raceforlifesponsorme.org/5th-floor
>> ________________________________________
>> From: 3view-bounces at open-em.org [3view-bounces at open-em.org] on behalf
>> of 3v=
>> iew-request at open-em.org [3view-request at open-em.org]
>> Sent: 07 October 2014 20:42
>> To: 3view at open-em.org
>> Subject: 3view Digest, Vol 4, Issue 2
>>
>> Send 3view mailing list submissions to
>>         3view at open-em.org
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>>         http://open-em.org/mailman/listinfo/3view
>> or, via email, send a message with subject or body 'help' to
>>         3view-request at open-em.org
>>
>> You can reach the person managing the list at
>>         3view-owner at open-em.org
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of 3view digest..."
>>
>>
>> Today's Topics:
>>
>>    1. Re: movement of the 3View knife (Tobias Starborg)
>>    2. Re: movement of the 3View knife (J?rgen Kornfeld)
>>    3. Re: movement of the 3View knife (Jean-Marc Verbavatz)
>>    4. Re: movement of the 3View knife (Tobias Starborg)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Tue, 7 Oct 2014 13:32:07 +0000
>> From: Tobias Starborg <tobias.starborg at manchester.ac.uk>
>> To: Mailing list for Gatan 3View Serial Block-Facing
>>         <3view at open-em.org>
>> Subject: Re: [3view] movement of the 3View knife
>> Message-ID: <D059A8A0.2C317%tobias.starborg at manchester.ac.uk>
>> Content-Type: text/plain; charset=3D"iso-8859-1"
>>
>> Hi Saskia,  I have seen this at least once, though I was showing the
>> people=
>>  the system, so didn't have a chance to look into it.  I get a similar
>> effe=
>> ct if I move the knife to 600?m (for example), then change my mind and
>> try =
>> to move to 500?m without going back to the retract position.
>>
>> Mine did clear initially, but restarted during approach.  I ended up
>> restar=
>> ting the 3 boxes and it was fine after that.  I've not seen it since.
>>
>> No errors that I can remember, though I was a bit flustered as I had
>> lots o=
>> f people keen to see their data in the room, so my main concern was to
>> get =
>> it working quickly rather than trouble shoot.
>>
>> Not sure that helps, but at least we have more than one occurrence.
>>
>> TS
>> --
>> Dr Tobias Starborg
>> Senior Experimental Officer: 3DEM
>> Wellcome Centre for Cell Matrix Research
>> Michael Smith Building
>> Manchester
>> M13 9PT
>> Tel: +44(0)1612755170
>> http://www.polara.manchester.ac.uk
>>
>>
>> From: Saskia Lippens
>> <Saskia.Lippens at irc.vib-ugent.be<mailto:Saskia.Lippens=
>> @irc.vib-ugent.be>>
>> Reply-To: Mailing list for Gatan 3View Serial Block-Facing
>> <3view at open-em.o=
>> rg<mailto:3view at open-em.org>>
>> Date: Tuesday, 7 October 2014 12:27
>> To: "3view at open-em.org<mailto:3view at open-em.org>"
>> <3view at open-em.org<mailto=
>> :3view at open-em.org>>
>> Subject: [3view] movement of the 3View knife
>>
>> Hi everyone,
>>
>> in Ghent we noticed that the horizontal movement of the 3View knife
>> (from 0=
>> -1200 um) is not always occurring in 1 smooth stroke, but the knife
>> stops f=
>> or a brief moment in 2 positions. We noticed this during the approach.
>> When=
>>  we stop the cutting and restart the 'phenomenon' does not take place
>> anymo=
>> re. Of course, we want to be sure that this does not happen during the
>> actu=
>> al acquisition.
>> Has anyone noticed this before?
>>
>> Thank you for your response,
>>
>> Saskia
>>
>>
>>
>>
>> Saskia Lippens, Ph.D.
>> Outreach Coordinator
>> FVMS Building - VIB
>> Technologiepark 927
>> 9052 Zwijnaarde
>> Belgium
>> +32-9/33.13.612
>> Saskia.Lippens at irc.vib-UGent.be<mailto:Saskia.Lippens at irc.vib-UGent.be>
>>
>>
>> [cid:285C07E9-B1A3-459F-95D6-D3A199704CB5 at irc.ugent.be][cid:3063916E-D9FE-4=
>>
>> A8B-A003-F05DD36EE6A1 at irc.ugent.be]
>>
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>> ------------------------------
>>
>> Message: 2
>> Date: Tue, 07 Oct 2014 16:02:26 +0200
>> From: J?rgen Kornfeld  <Joergen.Kornfeld at mpimf-heidelberg.mpg.de>
>> To: 3view at open-em.org
>> Subject: Re: [3view] movement of the 3View knife
>> Message-ID: <5433F272.8010604 at mpimf-heidelberg.mpg.de>
>> Content-Type: text/plain; charset=3DISO-8859-1; format=3Dflowed
>>
>> Hi all,
>>
>> if I understood correctly, this could be a broken cutter piezo
>> ("stuttering" of the knife while performing the cut instead of a smooth
>> movement). It is certainly not normal IMO if it happens during
>> continuous approaching. I've seen this once and replacing the cutter
>> piezo fixed the problem.
>>
>> Best regards,
>>
>> J?rgen
>>
>> Am 07.10.2014 15:19, schrieb Ilya Belevich:
>>> Hi Saskia,
>>>
>>> I have not seen anything like that on our system. For how long it stays?
>>>
>>> Best regards,
>>>
>>> Ilya
>>>
>>> --------------------------------------------------------------
>>>
>>> Ilya Belevich, PhD
>>>
>>> Electron Microscopy Unit
>>>
>>> Inst. of Biotechnology       phone: +358-2-941-59497
>>>
>>> PL56 (Viikinkaari 9)         email: ilya.belevich(AT)helsinki.fi
>>>
>>> University of Helsinki
>>>
>>> 00014 FINLAND                web:   www.biocenter.helsinki.fi/~ibelev
>>>
>>> *From:*3view-bounces at open-em.org [mailto:3view-bounces at open-em.org] *On
>>> Behalf Of *Saskia Lippens
>>> *Sent:* 07 October 2014 14:27
>>> *To:* 3view at open-em.org
>>> *Subject:* [3view] movement of the 3View knife
>>>
>>> Hi everyone,
>>>
>>> in Ghent we noticed that the horizontal movement of the 3View knife
>>> (from 0-1200 um) is not always occurring in 1 smooth stroke, but the
>>> knife stops for a brief moment in 2 positions. We noticed this during
>>> the approach. When we stop the cutting and restart the 'phenomenon' does
>>> not take place anymore. Of course, we want to be sure that this does not
>>> happen during the actual acquisition.
>>>
>>> Has anyone noticed this before?
>>>
>>> Thank you for your response,
>>>
>>> Saskia
>>>
>>> Saskia Lippens, Ph.D.
>>>
>>> Outreach Coordinator
>>>
>>> FVMS Building - VIB
>>>
>>> Technologiepark 927
>>>
>>> 9052 Zwijnaarde
>>>
>>> Belgium
>>>
>>> +32-9/33.13.612
>>>
>>> Saskia.Lippens at irc.vib-UGent.be <mailto:Saskia.Lippens at irc.vib-UGent.be>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> 3view mailing list
>>> 3view at open-em.org
>>> http://open-em.org/mailman/listinfo/3view
>>>
>>
>>
>> --
>> Joergen Kornfeld
>> +491799108803
>> Max-Planck-Institute for Medical Research
>> Jahnstrasse 29
>> 69120 Heidelberg, Germany
>>
>>
>> ------------------------------
>>
>> Message: 3
>> Date: Tue, 7 Oct 2014 20:33:55 +0200 (MEST)
>> From: "Jean-Marc Verbavatz" <verbavat at mpi-cbg.de>
>> To: "Mailing list for Gatan 3View Serial Block-Facing"
>>         <3view at open-em.org>
>> Subject: Re: [3view] movement of the 3View knife
>> Message-ID: <57222.10.1.130.29.1412706835.squirrel at webmail.mpi-cbg.de>
>> Content-Type: text/plain;charset=3Diso-8859-1
>>
>> Hi,
>>
>>> people the system, so didn't have a chance to look into it.  I get a
>>> similar effect if I move the knife to 600?m (for example), then
>>> change my
>>> mind and try to move to 500?m without going back to the retract
>>> position.
>>
>> On our system if i move to 600?m (or any value in the range) and then
>> want
>> to change to another position, whatever it is, i have to retract first:
>> otherwise the knife doesn't move at all ...
>> A little surprising first but not a major problem, unlike the knife
>> stopping in the middle of a cut !
>>
>> Cheers,
>>
>> jean-Marc
>>
>>> Mine did clear initially, but restarted during approach.  I ended up
>>> restarting the 3 boxes and it was fine after that.  I've not seen it
>>> since.
>>>
>>> No errors that I can remember, though I was a bit flustered as I had
>>> lots
>>> of people keen to see their data in the room, so my main concern was to
>>> get it working quickly rather than trouble shoot.
>>>
>>> Not sure that helps, but at least we have more than one occurrence.
>>>
>>> TS
>>> --
>>> Dr Tobias Starborg
>>> Senior Experimental Officer: 3DEM
>>> Wellcome Centre for Cell Matrix Research
>>> Michael Smith Building
>>> Manchester
>>> M13 9PT
>>> Tel: +44(0)1612755170
>>> http://www.polara.manchester.ac.uk
>>>
>>>
>>> From: Saskia Lippens
>>> <Saskia.Lippens at irc.vib-ugent.be<mailto:Saskia.Lippens at irc.vib-ugent.be>>
>>>
>>> Reply-To: Mailing list for Gatan 3View Serial Block-Facing
>>> <3view at open-em.org<mailto:3view at open-em.org>>
>>> Date: Tuesday, 7 October 2014 12:27
>>> To: "3view at open-em.org<mailto:3view at open-em.org>"
>>> <3view at open-em.org<mailto:3view at open-em.org>>
>>> Subject: [3view] movement of the 3View knife
>>>
>>> Hi everyone,
>>>
>>> in Ghent we noticed that the horizontal movement of the 3View knife
>>> (from
>>> 0-1200 um) is not always occurring in 1 smooth stroke, but the knife
>>> stop=
>> s
>>> for a brief moment in 2 positions. We noticed this during the approach.
>>> When we stop the cutting and restart the 'phenomenon' does not take
>>> place
>>> anymore. Of course, we want to be sure that this does not happen during
>>> the actual acquisition.
>>> Has anyone noticed this before?
>>>
>>> Thank you for your response,
>>>
>>> Saskia
>>>
>>>
>>>
>>>
>>> Saskia Lippens, Ph.D.
>>> Outreach Coordinator
>>> FVMS Building - VIB
>>> Technologiepark 927
>>> 9052 Zwijnaarde
>>> Belgium
>>> +32-9/33.13.612
>>> Saskia.Lippens at irc.vib-UGent.be<mailto:Saskia.Lippens at irc.vib-UGent.be>
>>>
>>>
>>> [cid:285C07E9-B1A3-459F-95D6-D3A199704CB5 at irc.ugent.be][cid:3063916E-D9FE=
>>>
>> -4A8B-A003-F05DD36EE6A1 at irc.ugent.be]
>>>
>>> _______________________________________________
>>> 3view mailing list
>>> 3view at open-em.org
>>> http://open-em.org/mailman/listinfo/3view
>>>
>>
>>
>> --
>> Jean-Marc Verbavatz
>> EM Leader
>> MPI-CBG
>> Pfotenhauerstra?e 108
>> 01307 Dresden
>> Germany
>> Tel: +49 351 210 1760
>> Fax: +49-351-210-1689
>> --
>> DRESDEN-concept Technology Platform: https://tp.dresden-concept.de
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 4
>> Date: Tue, 7 Oct 2014 19:42:22 +0000
>> From: Tobias Starborg <tobias.starborg at manchester.ac.uk>
>> To: Mailing list for Gatan 3View Serial Block-Facing
>>         <3view at open-em.org>
>> Subject: Re: [3view] movement of the 3View knife
>> Message-ID:
>> <72B0FA1F4D0BCE43B32E5CAD932BBAC50155F76ED7 at MBXP05.ds.man.ac.uk>
>> Content-Type: text/plain; charset=3D"iso-8859-1"
>>
>> Jean-Marc,
>>      Perhaps they've changed this since we got our system (hardware,
>> or sof=
>> tware version).  From my tomography days I realise that all the
>> mechanisms =
>> have a hysteresis, so its not logical to go backwards and forwards,
>> but I d=
>> o like to play and found it by accident as I wanted to align to a
>> different=
>>  part of the block face.
>>
>> TS
>>
>>
>> Dr Tobias Starborg
>> Senior Experimental Officer: 3DEM
>> Wellcome Centre for Cell Matrix Research
>> Michael Smith Building
>> Manchester
>> M13 9PT
>> Tel: +44(0)1612755170
>> http://www.polara.manchester.ac.uk
>>
>> ________________________________________
>> From: 3view-bounces at open-em.org [3view-bounces at open-em.org] on behalf
>> of Je=
>> an-Marc Verbavatz [verbavat at mpi-cbg.de]
>> Sent: 07 October 2014 19:33
>> To: Mailing list for Gatan 3View Serial Block-Facing
>> Subject: Re: [3view] movement of the 3View knife
>>
>> Hi,
>>
>>> people the system, so didn't have a chance to look into it.  I get a
>>> similar effect if I move the knife to 600?m (for example), then
>>> change my
>>> mind and try to move to 500?m without going back to the retract
>>> position.
>>
>> On our system if i move to 600?m (or any value in the range) and then
>> want
>> to change to another position, whatever it is, i have to retract first:
>> otherwise the knife doesn't move at all ...
>> A little surprising first but not a major problem, unlike the knife
>> stopping in the middle of a cut !
>>
>> Cheers,
>>
>> jean-Marc
>>
>>> Mine did clear initially, but restarted during approach.  I ended up
>>> restarting the 3 boxes and it was fine after that.  I've not seen it
>>> since.
>>>
>>> No errors that I can remember, though I was a bit flustered as I had
>>> lots
>>> of people keen to see their data in the room, so my main concern was to
>>> get it working quickly rather than trouble shoot.
>>>
>>> Not sure that helps, but at least we have more than one occurrence.
>>>
>>> TS
>>> --
>>> Dr Tobias Starborg
>>> Senior Experimental Officer: 3DEM
>>> Wellcome Centre for Cell Matrix Research
>>> Michael Smith Building
>>> Manchester
>>> M13 9PT
>>> Tel: +44(0)1612755170
>>> http://www.polara.manchester.ac.uk
>>>
>>>
>>> From: Saskia Lippens
>>> <Saskia.Lippens at irc.vib-ugent.be<mailto:Saskia.Lippens at irc.vib-ugent.be>>
>>>
>>> Reply-To: Mailing list for Gatan 3View Serial Block-Facing
>>> <3view at open-em.org<mailto:3view at open-em.org>>
>>> Date: Tuesday, 7 October 2014 12:27
>>> To: "3view at open-em.org<mailto:3view at open-em.org>"
>>> <3view at open-em.org<mailto:3view at open-em.org>>
>>> Subject: [3view] movement of the 3View knife
>>>
>>> Hi everyone,
>>>
>>> in Ghent we noticed that the horizontal movement of the 3View knife
>>> (from
>>> 0-1200 um) is not always occurring in 1 smooth stroke, but the knife
>>> stop=
>> s
>>> for a brief moment in 2 positions. We noticed this during the approach.
>>> When we stop the cutting and restart the 'phenomenon' does not take
>>> place
>>> anymore. Of course, we want to be sure that this does not happen during
>>> the actual acquisition.
>>> Has anyone noticed this before?
>>>
>>> Thank you for your response,
>>>
>>> Saskia
>>>
>>>
>>>
>>>
>>> Saskia Lippens, Ph.D.
>>> Outreach Coordinator
>>> FVMS Building - VIB
>>> Technologiepark 927
>>> 9052 Zwijnaarde
>>> Belgium
>>> +32-9/33.13.612
>>> Saskia.Lippens at irc.vib-UGent.be<mailto:Saskia.Lippens at irc.vib-UGent.be>
>>>
>>>
>>> [cid:285C07E9-B1A3-459F-95D6-D3A199704CB5 at irc.ugent.be][cid:3063916E-D9FE=
>>>
>> -4A8B-A003-F05DD36EE6A1 at irc.ugent.be]
>>>
>>> _______________________________________________
>>> 3view mailing list
>>> 3view at open-em.org
>>> http://open-em.org/mailman/listinfo/3view
>>>
>>
>>
>> --
>> Jean-Marc Verbavatz
>> EM Leader
>> MPI-CBG
>> Pfotenhauerstra?e 108
>> 01307 Dresden
>> Germany
>> Tel: +49 351 210 1760
>> Fax: +49-351-210-1689
>> --
>> DRESDEN-concept Technology Platform: https://tp.dresden-concept.de
>>
>>
>> _______________________________________________
>> 3view mailing list
>> 3view at open-em.org
>> http://open-em.org/mailman/listinfo/3view
>>
>>
>> ------------------------------
>>
>> _______________________________________________
>> 3view mailing list
>> 3view at open-em.org
>> http://open-em.org/mailman/listinfo/3view
>>
>>
>> End of 3view Digest, Vol 4, Issue 2
>> ***********************************
>>
>>
>> _______________________________________________
>> 3view mailing list
>> 3view at open-em.org
>> http://open-em.org/mailman/listinfo/3view
> _______________________________________________
> 3view mailing list
> 3view at open-em.org
> http://open-em.org/mailman/listinfo/3view


-- 
Joergen Kornfeld
+491799108803
Max-Planck-Institute for Medical Research
Jahnstrasse 29
69120 Heidelberg, Germany


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