Re: [micro-manager-general] Micro-manager and arduino

[Alexandre L. <ale...@gm...>]

Hello,

In the link I provided you I wanted you to see this image, specifically the
colors of the pins.

[image: image.png]

What I would do I if I were you, is check in the manual of the camera what
type of cable you are looking for that fits here.
This should be identical plug/socket should be in your camera right?

If you order that cable then you can attach those pins in your arduino for
him to send the trigger signal.
If you have an Arduino Uno, I suggest that you use the pins green, purple
and black in the image, in Arduino pins 12, 13 and GND, respectively.

On the webpage Luciano provided, there is this sub-page
https://sites.google.com/site/openspinmicroscopy/home/sub-systems/sample-rotation


which talks about sample rotation. besides the stepper motor you should
also have the red board in the circuits section and the power supply (12V).
That should handle the rotation part.

That link is very thorough and also has a link to a firmware that allows
you to rotate your sample. That code should be the one that you would use
in the Arduino.
You should install arduino software, load that code in the software; locate
the Arduino board (select usb port) and load.

When you get to this part mail me again, because there are a bunch of
options that you should know before going on, like the angle you are
considering for each shot, etc.
And also I'm kind of stuck in understanding this part.

Let me know if you have any issues

Alexandre Lopes


On Fri, 20 Mar 2020 at 22:29, Cindy Munoz <cmm...@gm...> wrote:

> Hi Alexander,
>
> I it seems the link you provided is broken. Also, do you know of any
> arduino codes out there that would work for this? I'm not an expert coder
> and struggle with basic things, but I want to learn.
>
> Thanks,
> Cindy
>
>
> On Fri, Mar 20, 2020, 5:45 AM Alexandre Lopes <ale...@gm...>
> wrote:
>
>> Hello Cindy,
>>
>> It's possible. What you would have to do is to use the Arduino to send
>> trigger signals so that the camera and rotate the camera.
>>
>> In one of the pdf manuals from FLIR. I suppose that you have the USB3
>> camera
>>
>> https://flir.app.boxcn.net/s/3u6ga43i3pidmi21x06yurccatal1qm5/file/416958602352
>>  you can see that if you have to use the green pin to send the trigger
>> signal (just on/off) from the Arduino to the camera and the black for
>> ground.
>>
>> Let me know if you have any issues. I am as well interested in this.
>>
>> Alexandre Lopes
>>
>>
>> On Fri, 20 Mar 2020 at 10:35, Carlos G Mendioroz <tr...@ac...> wrote:
>>
>>> Cindy Munoz @ 19/03/2020 19:04 -0300 dixit:
>>> > Hello everyone,  I have a unique imaging application that I'm trying to
>>> > develop with the help of Micro manager so that I have less image data
>>> > and steps to go through.
>>> >
>>> >  I have a stepper motor that is used to rotate a vial and to image I
>>> > have a ccd camera. I will be using fluorescence staining to image some
>>> > particles inside the vial and want to image the entire surface of the
>>> > vial to image all particles in the vial. I use the step motor to rotate
>>> > the vial. I tried to do this using imageJ but I will have a lot of
>>> image
>>> > data to analyze and I'm trying to cut down on steps if possible.
>>> >
>>> > What I'm trying to do is to take an image at a specified motor position
>>> > and continue to do this until the vial has rotated one full revolution.
>>> > Then stitch all images together to get the entire surface of the vial
>>> > with minimized distortion.
>>> >
>>> >  I have a Point Grey Chameleon camera that I was able to configure in
>>> > micro manager. I was also able to connect an arduino using the micro
>>> > manager wiki and currently have this as a shutter. I have a separate
>>> > arduino to control the step motor. I'd like to sync both the motor and
>>> > micro manager so that at a specified position Micro manager takes a
>>> > picture, sends a signal to the motor, the motor moves again, then Micro
>>> > manager takes another picture. This  process would continue until one
>>> > entire revolution is completed. I'd like to know if something like this
>>> > could be done easily with Micro manager. I do not have coding or
>>> > electronics experience and all that I have done has been based on
>>> > reading tutorials online. If you can provide some insight into how I
>>> > would be able to do this or direct me to other tutorials I would highly
>>> > appreciate it.
>>> >
>>> > Thank you,
>>> > Quiroz-1
>>>
>>> Cindy,
>>> I'm not a micro-manager expert, but have had some recent experience in
>>> interfacing a position control device (a.k.a. stage) with it using an
>>> arduino, so may be of help to you:
>>>
>>> uM knows about stages, and is able to control x-y coordinates natively.
>>> If you forget about one dimension, it may be just ok to use x as a
>>> rotation magnitude. Then you could use the acquisition manager to do
>>> snaps at different angles. Stiching them is another issue.
>>>
>>> Stepper control leverages CNC code. There are various codes that could
>>> be used and in general implement a positioning/acting control language
>>> called gCode. Micromanager has native support (RAMPS) for a Sprinter
>>> controler. I tweeked GRBL (which fits in an arduino UNO) to be
>>> recognized by the RAMPS driver in uM.
>>>
>>> Look for info in the mailing list archives.
>>>
>>> --
>>> Carlos G Mendioroz  <tr...@ac...>
>>>
>>>
>>> _______________________________________________
>>> micro-manager-general mailing list
>>> mic...@li...
>>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>>>
>>