Problems with calibaration

[Timo B.]

Hi everybody,

I have some problems with the calibration of my pgFocus setup and with the pgFocus software.
My fist problem is, that the pgFocus.exe doesn't work. In the task manager I could see that it started the process javaw.exe but else it did nothing.
If I start the pgFocus.pde with Processing it started the pgFocus software, but if I try to calibrate or get the light profile the screen just turned white and Processing gave this massage:

selecting port: 0
COM15
Using Serial Port: COM15
Error, disabling serialEvent() for COM15
null

I also tried to calibrate the pgFocus in μManager, but after pressing the button it only changed from calibrate to processing without changing the outgoing voltage.
The only thing that worked fine was the Arduino IDE and after I calibrated there, I also could activate the focus stabilization in μManager.
I would really like to know why μManager and the pgFocus software dont work with my setup.

Thanks and best regards,
Timo

[Karl Bellve]

Hi Timo,

Is pgFocus on COM15? Is it set to the correct speed? 

I assume you were able to get pgFocus Device Adapter installed for µManager? If so, In pgFocus µManager device adapter, do you see something like this?

https://micro-manager.org/wiki/File:PgFocus_DeviceAdapter.png

Do you see something different?

It could be something as simple as line feed issues on the serial port or serial speed set incrorrecting. You can see on the above graphic, pgFocus appears to use \r\n. 

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Kia ora,

Karl Bellvé

Kia ora, a common Kiwi salutation, means to wish somebody life and health in the Maori language

[Timo B.]

Thanks for the fast response,

Yes, pgFocus was on COM15. Speed was set to 57600.

I think the window looked very similar except of course Exposure time, offset and things like that. On Monday I can send a picture of it.

Timo

[Timo B.]

So here the autofocus properties

[Karl Bellve]

Hi Timo,

Sorry if you already know this, but this has happened. Make sure you are only running either the pgFocus application (via processing), or µManager, not both. They can't be run at the same time.

Since you are able to run pgFocus application, via processing, you can export the exe from processing. There might be some incompatibilities from the original .exe and your system. File -> Export Application.

I think the key is getting the light profile, which appears to be happening at least in µManager.  From your image, the maximum intensity is only 35, and the min is 27. Which means there is no peak. You might not have a coverslip on, or pgFocus might not be aligned yet.

With µManager, can you switch tabs to 'Light Profile' https://micro-manager.org/wiki/File:PgFovus_Lightprofile.png

I assume you will see a flat line...but do you see anything?

pgFocus will only do a calibration if it sees a peak.

BTW, I will be out of town until Friday.

On Mon, Aug 26, 2019 at 5:22 AM Timo B. <eckr...@gmail.com> wrote:

So here the autofocus properties

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[Timo B.]

Am Montag, 26. August 2019 17:01:07 UTC+2 schrieb Karl Bellve:

Hi Timo,

Sorry if you already know this, but this has happened. Make sure you are only running either the pgFocus application (via processing), or µManager, not both. They can't be run at the same time.

Yes, I considered this already.

 

Since you are able to run pgFocus application, via processing, you can export the exe from processing. There might be some incompatibilities from the original .exe and your system. File -> Export Application.

This worked fine. I just had to copie the Kiwi picture in the right folder.

 

I think the key is getting the light profile, which appears to be happening at least in µManager.  From your image, the maximum intensity is only 35, and the min is 27. Which means there is no peak. You might not have a coverslip on, or pgFocus might not be aligned yet.

With µManager, can you switch tabs to 'Light Profile' https://micro-manager.org/wiki/File:PgFovus_Lightprofile.png

I assume you will see a flat line...but do you see anything?

Yes, I have a light profile, I just took the picture while I had the Laser off. But at the moment the profile is a bit broad.

 

pgFocus will only do a calibration if it sees a peak.

BTW, I will be out of town until Friday.

Is there a difference between the calibration in µManager and in the terminal, because in the terminal it could see a peak and it also stabelized after the calibration?

 

On Mon, Aug 26, 2019 at 5:22 AM Timo B. <eckr...@gmail.com> wrote:

So here the autofocus properties

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[Karl Bellve]

On Tue, Aug 27, 2019 at 5:15 AM Timo B. <eckr...@gmail.com> wrote:

Is there a difference between the calibration in µManager and in the terminal, because in the terminal it could see a peak and it also stabelized after the calibration?

 

Timo, sorry for the delayed reply.

The calibration is actually done on the hardware itself, and the values from that calibration is stored on the hardware as well. All stored in non-volatile flash memory. 

The pgFocus application and µManager just initiates the calibration. Once the calibration has been done, it doesn't have to be repeated, unless something changes in pgFocus' optical path. 

I will check the pgFocus application and see if there are any issues there with initiating calibration...