[OpenSPIM] Picard stage error after update

Thu Aug 21 05:26:24 CDT 2014

Hi Luke,

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 31st) 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!

Regards,
Veli-Pekka

From: Luke Stuyvenberg [mailto:stuyvenberg at wisc.edu]
Sent: 21. elokuuta 2014 5:20
To: Veli-Pekka Ronkainen; openspim at openspim.org
Subject: Re: VS: [OpenSPIM] Picard stage error after update

Hi Veli-Pekka,

On 8/18/2014 4:18 AM, Veli-Pekka Ronkainen wrote:

Hi Luke,

Thanks for your reply! I attach here different CoreLogs created by two different software versions:
Thanks! These have really helped.

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).
>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 Probably this is because the version of mmgr_dal_PicardStage.dll is out-of-date, and only checks the serial numbers up to 250.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 I will try to upload a newer version of the DAL to the update site, once I'm sure it's compatible.

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.
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).

The last CoreLog (no pid number) is generated by the non-updated SW version downloaded from openspim.org. Here everything is fine.

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?
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.)

I hope this all helps, and I'll see what I can do about causing a more permanent change. Thanks!

Luke

On 8/18/2014 4:18 AM, Veli-Pekka Ronkainen wrote:

Hi Luke,

Thanks for your reply! I attach here different CoreLogs created by two different software versions:

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).

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.

The last CoreLog (no pid number) is generated by the non-updated SW version downloaded from openspim.org. Here everything is fine.

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?

Regards,

Veli-Pekka

________________________________
Lähettäjä: openspim-bounces at openspim.org<mailto:openspim-bounces at openspim.org> <openspim-bounces at openspim.org><mailto:openspim-bounces at openspim.org> käyttäjän puolestaLuke Stuyvenberg <stuyvenberg at wisc.edu><mailto:stuyvenberg at wisc.edu>
Lähetetty: 16. elokuuta 2014 4:10
Vastaanottaja: openspim at openspim.org<mailto:openspim at openspim.org>
Aihe: Re: [OpenSPIM] Picard stage error after update

Hi Veli-Pekka,

On 8/14/2014 7:01 AM, Veli-Pekka Ronkainen wrote:
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: http://openspim.org/pipermail/openspim/2014-July/000482.html .
As you suspected, this is because of the change in step size.
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.
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.

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

"Device,Picard Twister,StepSize,1.8"

Changing the 1.8 to 1 should resolve at least the rotational stage problem.

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!
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.

Hope this helps,
Luke Stuyvenberg

P.S. If you get a few moments, please feel free to update http://openspim.org/Who_has_an_OpenSPIM%3F with your location and information! We love hearing about people using the system.

On 8/14/2014 7:01 AM, Veli-Pekka Ronkainen wrote:

Dear all,

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!

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: http://openspim.org/pipermail/openspim/2014-July/000482.html . 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.

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!

Regards,

Veli-Pekka Ronkainen

Light Microscopy Core Facility

Biocenter Oulu, University of Oulu

Finland

_______________________________________________

OpenSPIM mailing list

OpenSPIM at openspim.org<mailto:OpenSPIM at openspim.org>

http://openspim.org/mailman/listinfo/openspim

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://openspim.org/pipermail/openspim/attachments/20140821/0cbd312d/attachment-0001.html>