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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hi Luke,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thanks again! It’s nice to hear some logic behind these errors, and I think this solved the problem! Amazing, but earlier we copied that mmgr_dal_PicardStage.dll
from µManager recent “nightly build” and it did not work. Now we copied the file from the latest 1.4.18 –release (July 31<sup>st</sup>) and everything works fine. We can create new configurations and modify old ones. Also twister rotation angles correspond
with the angle adjustments made in the “acquire spim images” –plugin even without modifying the old .cfg –file. I’m not sure what was the role of a very recent update of the acquire spim images -plugin that we installed just before testing. I hope you find
some good general solution, but for us all good for now, thank you very much!<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Veli-Pekka<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext"> Luke Stuyvenberg [mailto:stuyvenberg@wisc.edu]
<br>
<b>Sent:</b> 21. elokuuta 2014 5:20<br>
<b>To:</b> Veli-Pekka Ronkainen; openspim@openspim.org<br>
<b>Subject:</b> Re: VS: [OpenSPIM] Picard stage error after update<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hi Veli-Pekka,<br>
<br>
On 8/18/2014 4:18 AM, Veli-Pekka Ronkainen wrote:<o:p></o:p></p>
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<p style="background:white"><span style="font-family:"Calibri","sans-serif"">Hi Luke,<o:p></o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri","sans-serif""><o:p> </o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri","sans-serif"">Thanks for your reply! I attach here different CoreLogs created by two different software versions:<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">Thanks! These have really helped.<o:p></o:p></p>
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<p style="background:white"><span style="font-family:"Calibri","sans-serif"">The first CoreLog pid3156 is generated by the latest SW version. Here we tried to make a new configuration and adding/editing Picard Z-stage is not possible [IFO,dev:Picard Z Stage]
Could not initialize motor -1 (PiUsb error code 1). <o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">From the core log, I see the line "2014-08-18T09:27:19.082080 tid860 [IFO,dev:Picard Twister] Found 0 motors and 1 twisters." -- in essence, it isn't finding any of your stages. Probably this is because the
version of mmgr_dal_PicardStage.dll is out-of-date, and only checks the serial numbers up to 250. (A newer version is available in vanilla Micro-Manager that checks up to 500, and I've been looking into a more reasonable detector that should discover any regardless
of serial number...) I will try to upload a newer version of the DAL to the update site, once I'm sure it's compatible.<o:p></o:p></p>
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<p style="background:white"><span style="font-family:"Calibri","sans-serif"">The next one pid4032 is generated by the same SW version, and we tried to modify an existing older .cfg-file which is also attached here.
<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">Another odd issue. I think it's related, but I'm not totally sure how -- something about the first failure to communicate with the stage seems to trigger a series of Java errors referring to the rest of the
devices in the configuration (I think).<o:p></o:p></p>
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<div>
<p style="background:white"><span style="font-family:"Calibri","sans-serif"">The last CoreLog (no pid number) is generated by the non-updated SW version downloaded from openspim.org. Here everything is fine.
<o:p></o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri","sans-serif""> <o:p>
</o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri","sans-serif"">There is no possibility to edit the old .cfg-file with notepad like you suggested, since there is no mention about the Twister step size. Maybe because there is no possibility to edit step
sizes in the older SW version, only serial numbers? <o:p></o:p></span></p>
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<p class="MsoNormal">You're probably right. It may work to simply add the line I mentioned, only with the '1' instead of '1.8'. (Again, this isn't a fix for the underlying problem, but I'll be looking at that.)<br>
<br>
I hope this all helps, and I'll see what I can do about causing a more permanent change. Thanks!<br>
<br>
Luke<br>
<br>
On 8/18/2014 4:18 AM, Veli-Pekka Ronkainen wrote:<o:p></o:p></p>
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<p style="background:white"><span style="font-family:"Calibri","sans-serif"">Hi Luke,<o:p></o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri","sans-serif""><o:p> </o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri","sans-serif"">Thanks for your reply! I attach here different CoreLogs created by two different software versions:<o:p></o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri","sans-serif""><o:p> </o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri","sans-serif"">The first CoreLog pid3156 is generated by the latest SW version. Here we tried to make a new configuration and adding/editing Picard Z-stage is not possible [IFO,dev:Picard Z Stage]
Could not initialize motor -1 (PiUsb error code 1). <o:p></o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri","sans-serif""><o:p> </o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri","sans-serif"">The next one pid4032 is generated by the same SW version, and we tried to modify an existing older .cfg-file which is also attached here.
<o:p></o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri","sans-serif""><o:p> </o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri","sans-serif"">The last CoreLog (no pid number) is generated by the non-updated SW version downloaded from openspim.org. Here everything is fine.
<o:p></o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri","sans-serif""> <o:p>
</o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri","sans-serif"">There is no possibility to edit the old .cfg-file with notepad like you suggested, since there is no mention about the Twister step size. Maybe because there is no possibility to edit step
sizes in the older SW version, only serial numbers? <o:p></o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri","sans-serif""><o:p> </o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri","sans-serif"">Regards,<o:p></o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri","sans-serif"">Veli-Pekka<o:p></o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri","sans-serif""><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><b><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Lähettäjä:</span></b><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">
<a href="mailto:openspim-bounces@openspim.org">openspim-bounces@openspim.org</a> <a href="mailto:openspim-bounces@openspim.org">
<openspim-bounces@openspim.org></a> käyttäjän puolestaLuke Stuyvenberg <a href="mailto:stuyvenberg@wisc.edu">
<stuyvenberg@wisc.edu></a><br>
<b>Lähetetty:</b> 16. elokuuta 2014 4:10<br>
<b>Vastaanottaja:</b> <a href="mailto:openspim@openspim.org">openspim@openspim.org</a><br>
<b>Aihe:</b> Re: [OpenSPIM] Picard stage error after update</span><span style="font-family:"Calibri","sans-serif";color:#282828">
<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Calibri","sans-serif";color:#282828"> <o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Calibri","sans-serif";color:#282828">Hi Veli-Pekka,<br>
<br>
On 8/14/2014 7:01 AM, Veli-Pekka Ronkainen wrote:<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-family:"Calibri","sans-serif";color:#282828">However, now after using the Fiji updater Picard USB-stage rotation angle coordinates are not right anymore. Changing angle from -180 deg to 180 deg
rotates the sample holder only ~180 degrees, and rotation in general spins the sample much less than indicated by the slider. In addition, we can not access and modify old .cfg-files, so that it would be possible to change step size of the twister from 1.8
to 1, as it was discussed earlier: <a href="http://openspim.org/pipermail/openspim/2014-July/000482.html">
http://openspim.org/pipermail/openspim/2014-July/000482.html</a> .<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:12.0pt;background:white"><span style="font-family:"Calibri","sans-serif";color:#282828">As you suspected, this is because of the change in step size.<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-family:"Calibri","sans-serif";color:#282828">Modification of an existing configuration starts with an error "Error in device Picard Z Stage: Unable to communicate with the device" followed by lots
of COM and "No device with label _device name_" -errors. Creating a new configuration doesn't help since it is not possible to add Picard stage z-axis to the config file or modify the serial number.
<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:12.0pt;background:white"><span style="font-family:"Calibri","sans-serif";color:#282828">The error when modifying a configuration or creating new configurations is a different problem entirely, and one I wasn't aware
of. If you could, please, attach a CoreLog or two from after the update, when you've received these errors. (If you can't tell which one contains these errors, you can open them and search, or just run the program again and produce a new one.) This would go
a long way towards figuring out what's causing this problem.<br>
<br>
But in the meantime, an easy, dirty solution to the problem interfering with your experiments is to open a working configuration file in Notepad. You should see a line in there that reads something like<br>
<br>
"Device,Picard Twister,StepSize,1.8"<br>
<br>
Changing the 1.8 to 1 should resolve at least the rotational stage problem.<o:p></o:p></span></p>
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<p style="background:white"><span style="font-family:"Calibri","sans-serif"">We've tried to copy the latest Picard .dll-files from the recent Micro-Manager nightly build but the problem persists. Are there some other files we should copy and replace as well?
Of course we can still download and configure the non-updated package from openspim.org and be happy using that older version without any problems. Still it would be nice to be up-to-date. Anyone having the same problems or some solutions? Thanks!<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Calibri","sans-serif";color:#282828">You shouldn't need any other files; hopefully the above is all it takes to get things running until I can figure out what's causing the trouble with
editing configurations.<br>
<br>
Hope this helps,<br>
Luke Stuyvenberg<br>
<br>
P.S. If you get a few moments, please feel free to update <a href="http://openspim.org/Who_has_an_OpenSPIM%3F">
http://openspim.org/Who_has_an_OpenSPIM%3F</a> with your location and information! We love hearing about people using the system.<br>
<br>
On 8/14/2014 7:01 AM, Veli-Pekka Ronkainen wrote:<o:p></o:p></span></p>
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<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
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<p style="background:white"><span style="font-family:"Calibri","sans-serif"">Dear all,<o:p></o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri","sans-serif""><o:p> </o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri","sans-serif"">We've been scanning some mouse tissue test samples with our dual-side illumination OpenSPIM for a short while now, and we are very happy with the first results!
<o:p></o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri","sans-serif""><o:p> </o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri","sans-serif"">We have used the original software package downloaded from openspim.org without any updates, and it has been working fine. However, now after using the Fiji updater Picard USB-stage
rotation angle coordinates are not right anymore. Changing angle from -180 deg to 180 deg rotates the sample holder only ~180 degrees, and rotation in general spins the sample much less than indicated by the slider. In addition, we can not access and modify
old .cfg-files, so that it would be possible to change step size of the twister from 1.8 to 1, as it was discussed earlier:
<a href="http://openspim.org/pipermail/openspim/2014-July/000482.html">http://openspim.org/pipermail/openspim/2014-July/000482.html</a> . Modification of an existing configuration starts with an error "Error in device Picard Z Stage: Unable to communicate with
the device" followed by lots of COM and "No device with label _device name_" -errors. Creating a new configuration doesn't help since it is not possible to add Picard stage z-axis to the config file or modify the serial number.
<o:p></o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri","sans-serif""><o:p> </o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri","sans-serif"">We've tried to copy the latest Picard .dll-files from the recent Micro-Manager nightly build but the problem persists. Are there some other files we should copy and replace as well?
Of course we can still download and configure the non-updated package from openspim.org and be happy using that older version without any problems. Still it would be nice to be up-to-date. Anyone having the same problems or some solutions? Thanks!<o:p></o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri","sans-serif""><o:p> </o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri","sans-serif"">Regards,<o:p></o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri","sans-serif"">Veli-Pekka Ronkainen<o:p></o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri","sans-serif"">Light Microscopy Core Facility
<o:p></o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri","sans-serif"">Biocenter Oulu, University of Oulu<o:p></o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri","sans-serif"">Finland<o:p></o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri","sans-serif""><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Calibri","sans-serif";color:#282828"><br>
<br>
<o:p></o:p></span></p>
<pre style="background:white"><span style="color:#282828">_______________________________________________<o:p></o:p></span></pre>
<pre style="background:white"><span style="color:#282828">OpenSPIM mailing list<o:p></o:p></span></pre>
<pre style="background:white"><span style="color:#282828"><a href="mailto:OpenSPIM@openspim.org">OpenSPIM@openspim.org</a><o:p></o:p></span></pre>
<pre style="background:white"><span style="color:#282828"><a href="http://openspim.org/mailman/listinfo/openspim">http://openspim.org/mailman/listinfo/openspim</a><o:p></o:p></span></pre>
</blockquote>
<p class="MsoNormal" style="background:white"><span style="font-family:"Calibri","sans-serif";color:#282828"><o:p> </o:p></span></p>
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</blockquote>
<p class="MsoNormal"><o:p> </o:p></p>
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