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

[Austin <adv...@gm...>]

Following up on this - 

Carlos Medinoroz noted the other option here would be to buy a RAMPS shield for your arduino and then use the RAMPS GCODE driver for micromanager. 
This would basically do everything I suggested below - but without the need for any custom programming.
I think this is a much better option for you!

RAMPS board project - https://reprap.org/wiki/RAMPS_1.6 <https://reprap.org/wiki/RAMPS_1.6>
GCODE driver for micromanager https://micro-manager.org/wiki/RAMPS <https://micro-manager.org/wiki/RAMPS>





Austin Blanco
Advanced Research Consulting Corporation
e. au...@au... <mailto:au...@au...>
w. www.advancedresearch.co <http://www.advancedresearch.co/>
c. 510.708.2995





> On Mar 20, 2020, at 7:00 AM, Austin <adv...@gm...> wrote:
> 
> I would do this using a script. 
> 
> On the Arduino side, what motor driver are you using? Consider the following:
> 
> Using 1 arduino only
> 	- arduino sends a signal to light source
> 	- arduino moves motor. 
> 
> Some questions
> 	Do you know where the rotting platform is empirically? In other words do you have any known position readout like a Zero or a rotary encoder attached?
> 	Do you always want to move the same amount on the motor per image? 
> 	Do you always want to move equal amounts?
> 	Do you want to change the number of moves per experiment?
> 
> I would set this up so that the order of operation is:
> 
> 1. Set motor to start position (either by hand if no position sensing is used, or using a command sent over serial from micromanager to the arduino, like “home”.)
> 2. Attach a runnable inside MM for the time domain, which has a serial command inside with something like “move 10” or whatever move command you want to use. 
> 	- be sure to include a delay so that the motor has time to move)
> 3. inside the arduino, have the Move # command perform the needed steps and output signals to motor and camera. 
> 4. configure a timelapse in micromanager MDA
> 5. run the timelapse. 
> 
> this way if you need to change timelapse duration or distance moved, its easy to change the runnable value, camera exposure, # of images in a sweep etc. 
> 
> If you’d like some assistance for this I can send you resources at no charge to get going. Don’t fear the Arduino code!!! With some basic knowledge it’s straightforward and very powerful to work with!!! 
> 
> 
> Austin Blanco
> Advanced Research Consulting Corporation
> e. au...@au... <mailto:au...@au...>
> w. www.advancedresearch.co <http://www.advancedresearch.co/>
> c. 510.708.2995
> 
> 
> 
> 
> 
>> On Mar 20, 2020, at 6:42 AM, Luciano Marpegan <luc...@gm... <mailto:luc...@gm...>> wrote:
>> 
>> Dear Cindy, I suggest you to check the openspin microscopy project I works with MManager and arduino and I think it does what you need.
>> https://sites.google.com/site/openspinmicroscopy/ <https://sites.google.com/site/openspinmicroscopy/>
>> Best,
>> Luciano
>> 
>> El vie., 20 mar. 2020 0:55, Cindy Munoz <cmm...@gm... <mailto:cmm...@gm...>> escribió:
>> 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
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