A few questions about my setup

[Kurt Kagan Kurtoglu]

Hey! I am currently working on desinging a setup to provide the stage movement through z-axis on TIRF (its schema is uploaded). So, I have a few questions:

1- In calibration process, what should be done on MicroManager?

2- When I put a mirror on the stage, I can easily see the back reflection coming from the beam splitter. I expect so when I align my objective and drop some immersion oil and put some water on a coverslip but it cannot be seen and also cannot be predictible where the beam goes using the objective instead of a mirror. Do you have any suggestions? As I said, back reflection beam is very dim. How can overcome this problem?

3- After doing all processes, what signs can show me that the sensor works well?

4- Lastly, should I change any of values on device control part on MicroManager?

Thanks for helps!

[Karl Bellve]

Replies below.

BTW, in case any is interested, I did design a pgFocus Shield, which should be immensely easier to make compared to a full blown pgFocus. I have never built or tested it myself.

On Sun, Jul 22, 2018 at 7:49 AM Kurt Kagan Kurtoglu <kkagank...@gmail.com> wrote:

Hey! I am currently working on desinging a setup to provide the stage movement through z-axis on TIRF (its schema is uploaded). So, I have a few questions:

1- In calibration process, what should be done on MicroManager?

I think it is better to do the initial setup and calibration in the pgFocus app. I can't recall what I did in uManager pgFocus plugin but it isn't as responsive :D 

The pgFocus apps shows a nice light profile as the beam is adjusted, and once you have a nice peak, you can run the calibration routine. The results are then saved in pgFocus firmware.  Command is 'c'

The only thing you need to look is making sure the piezo movement is known by pgFocus. The default is 1V/10µm.

 

2- When I put a mirror on the stage, I can easily see the back reflection coming from the beam splitter. I expect so when I align my objective and drop some immersion oil and put some water on a coverslip but it cannot be seen and also cannot be predictible where the beam goes using the objective instead of a mirror. Do you have any suggestions? As I said, back reflection beam is very dim. How can overcome this problem?

I use a Laser Viewing Card from Thorlabs like the VRC4. You could also use a visible laser until you have everything adjusted, and then swap lasers.

 

3- After doing all processes, what signs can show me that the sensor works well?

Make sure your board can communicate with the sensor. You should see a fairly flat light profile, assuming no or very little light. Expose the sensor to light. You can also print out the light profile with the 'l' command via serial port.

If you are doing the analog voltage, there is a command to do a voltage ramp. I think it is "t' to initiate the voltage ramp. Check on an oscilloscope. Also, check to see if your piezo is moving. 

 

4- Lastly, should I change any of values on device control part on MicroManager?

Just check Micron/Volt, which defaults to 10.

Good Luck!

 

Thanks for helps!

--
You received this message because you are subscribed to the Google Groups "pgFocus" group.
To unsubscribe from this group and stop receiving emails from it, send an email to pgfocus+u...@googlegroups.com.
To post to this group, send email to pgf...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/pgfocus/91acff8b-d484-4a10-b93a-fd5ea0ac8a3a%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Kurt Kagan Kurtoglu]

Thanks for your Response.

I just got the back reflection which was so dim. I can detect it with only my phone`s camera. Should I see the beam on a laser viewing card?

[Karl Bellve]

On Fri, Jul 27, 2018 at 5:53 AM Kurt Kagan Kurtoglu <kkagank...@gmail.com> wrote:

Thanks for your Response.

I just got the back reflection which was so dim. I can detect it with only my phone`s camera. Should I see the beam on a laser viewing card?

It is very dim, and it is very hard to see. I guess it depends on the laser power you are using. We normally aperture down the laser after pgFocus is installed, but we open up the aperture when we need to do any adjustments.

The pgFocus sensor is very sensitive, and pgFocus will adjust its exposure. The dimness of the return beam shouldn't be a problem.  The return beam must be in alignment with the sensor, as the return beam moves up and down the sensor.

Cheers Karl

[Kurt Kagan Kurtoglu]

Thank you for your kind reply.

My setup looks done. I connected all parts and expect to see light profile and to do calibration. However, what I get is only straight lines on micromanager. I also tried that on pgfocus and found no clues about the signal from my sensor array. So, during this process, I run the code on Processing script panel and as you know it directs me to pgfocus software. At this point, when I type 'l' or other letters, the script panel gives me an error on bottom which is attached below. By the way, all software parts are downloaded including Ardunio software.

Thanks!

[Karl Bellve]

Hi Kurt,

Did you install the Ardiuno Leonardo bootloader onto your pgFocus hardware?

I use an AVR programmer to upload the bootloader to pgFocus: https://www.adafruit.com/product/46 but you could also use another Arduino.

Did it work? If so, you should be able to use the normal Arduino IDE to run simple sketches that are available in the IDE. You should see communication.

When you get basic communication working, then you can upload pgFocus sketch and then test the commands, all inside the Arduino IDE.

http://big.umassmed.edu/wiki/index.php/PgFocus#Firmware

Cheers Karl

--

You received this message because you are subscribed to the Google Groups "pgFocus" group.
To unsubscribe from this group and stop receiving emails from it, send an email to pgfocus+u...@googlegroups.com.
To post to this group, send email to pgf...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/pgfocus/a39b0440-aee5-42ee-b5d6-98563a9385e5%40googlegroups.com.