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

[Cindy M. <cmm...@gm...>]

Awesome, thanks for the info! I will look into this.

Thanks,
Cindy

On Wed, Apr 1, 2020 at 12:39 PM Rusty Nicovich <rus...@gm...>
wrote:

> Our OPT does something very similar to the OpenSpin design, where an
> Arduino controls the stepper motor rotation (via a driver board) and can
> trigger an industrial CMOS camera (IDS, not PointGrey, but very similar
> connectors).  Our repo includes an Arudino sketch, MicroManager script, and
> PCB design for assembling such a system:
>
> https://github.com/AllenInstitute/AIBSOPT
>
> There would be a few small modifications to make to suit your needs, but
> the same equipment could easily handle rotating a motor w/ synchronized
> camera triggering.
>
> Thanks,
> Rusty
>
> On Sat, Mar 21, 2020 at 6:31 PM Alexandre Lopes <ale...@gm...>
> wrote:
>
>> 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...>
>>>>>
>>>>>
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>>>>>
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