Re: [micro-manager-general] Micro-manager and arduino
Carlos G Mendioroz
> 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...@acm.org>
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Kumar, Sunil
Hi Cindy,
I have written a Micro-manager plugin for doing OPT imaging, which basically does exactly this, except for the image stitching (we do backprojection to retrieve the volume instead). If you can control your motor as a z-stage device though, it should work – please get in touch if this might be of use, and I can send you a version to try if you wish, with some instructions.
Regards,
Sunil
From: Cindy Munoz [mailto:cmmm...@gmail.com]
Sent: 19 March 2020 22:05
To: micro-mana...@lists.sourceforge.net
Subject: [micro-manager-general] Micro-manager and arduino
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