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

[Kumar, S. <sun...@im...>]

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:cmm...@gm...]
Sent: 19 March 2020 22:05
To: mic...@li...
Subject: [micro-manager-general] Micro-manager and arduino

This email from cmm...@gm...<mailto:cmm...@gm...> originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list<https://spam.ic.ac.uk/SpamConsole/Senders.aspx> to disable email stamping for this address.


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