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

[Rusty N. <rus...@gm...>]

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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