Micro-manager and arduino

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Micro-manager and arduino

Quiroz1
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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Re: Micro-manager and arduino

tron
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  <[hidden email]>


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Re: Micro-manager and arduino

Sunil
In reply to this post by Quiroz1

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:[hidden email]]
Sent: 19 March 2020 22:05
To: [hidden email]
Subject: [micro-manager-general] Micro-manager and arduino

 

This email from [hidden email] 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 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



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Re: Micro-manager and arduino

Z H
In reply to this post by Quiroz1
Hi -- If like me you don't want to learn how to write and compile a new device adapter, the Arduino shutter adapter has a few outputs and inputs that you may not need. You can modify the Arduino sketch and your circuit to use these for other purposes. For example, we used some to control the color and brightness of a neopixel LED ring - https://github.com/zach-hensel/lasers-and-brightfield - it's a bit of a hack obviously but it sounds like something like this might work for your application.

Cheers,
Zach

On Fri, Mar 20, 2020, 03:55 Cindy Munoz <[hidden email]> wrote:
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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micro-manager-general mailing list
[hidden email]
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Re: Micro-manager and arduino

alexandrenpl
In reply to this post by tron
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
 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 <[hidden email]> 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  <[hidden email]>


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micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general


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Re: Micro-manager and arduino

Lumarpe
In reply to this post by Quiroz1
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.
Best,
Luciano

El vie., 20 mar. 2020 0:55, Cindy Munoz <[hidden email]> 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
_______________________________________________
micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general


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Re: Micro-manager and arduino

AustinBlanco
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. [hidden email]
w. www.advancedresearch.co
c. 510.708.2995





On Mar 20, 2020, at 6:42 AM, Luciano Marpegan <[hidden email]> 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.
Best,
Luciano

El vie., 20 mar. 2020 0:55, Cindy Munoz <[hidden email]> 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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Re: Spam (9.539):Re: Micro-manager and arduino

tron
Austin @ 20/03/2020 11:00 -0300 dixit:
> 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. 
>

Why would you distribute the control between an arduino and
micro-manager instead of centralizing the control on the later ?

--
Carlos G Mendioroz  <[hidden email]>


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Re: Micro-manager and arduino

AustinBlanco
In reply to this post by AustinBlanco
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
GCODE driver for micromanager https://micro-manager.org/wiki/RAMPS





Austin Blanco
Advanced Research Consulting Corporation
e. [hidden email]
w. www.advancedresearch.co
c. 510.708.2995





On Mar 20, 2020, at 7:00 AM, Austin <[hidden email]> 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. [hidden email]
w. www.advancedresearch.co
c. 510.708.2995





On Mar 20, 2020, at 6:42 AM, Luciano Marpegan <[hidden email]> 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.
Best,
Luciano

El vie., 20 mar. 2020 0:55, Cindy Munoz <[hidden email]> 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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Re: Micro-manager and arduino

Quiroz1
In reply to this post by alexandrenpl
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 <[hidden email]> 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
 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 <[hidden email]> 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  <[hidden email]>


_______________________________________________
micro-manager-general mailing list
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https://lists.sourceforge.net/lists/listinfo/micro-manager-general


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Re: Micro-manager and arduino

alexandrenpl
Hello,

In the link I provided you I wanted you to see this image, specifically the colors of the pins.

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

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 <[hidden email]> 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 <[hidden email]> 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
 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 <[hidden email]> 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  <[hidden email]>


_______________________________________________
micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general


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Re: Micro-manager and arduino

Lumarpe
In reply to this post by Quiroz1
Hi Cindy, have you checked the openspin project? It runs a MManager plugin and you would need not coding at all. It controls a spinning motor, xyz stage and can trigger hardware, all from a single arduino.
Best,
Luciano

El sáb., 21 mar. 2020 0:10, Cindy Munoz <[hidden email]> escribió:
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 <[hidden email]> 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
 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 <[hidden email]> 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  <[hidden email]>


_______________________________________________
micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general
_______________________________________________
micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general


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micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general
Reply | Threaded
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|

Re: Micro-manager and arduino

Ti_Sapph
In reply to this post by alexandrenpl
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 <[hidden email]> wrote:
Hello,

In the link I provided you I wanted you to see this image, specifically the colors of the pins.

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

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 <[hidden email]> 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 <[hidden email]> 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
 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 <[hidden email]> 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  <[hidden email]>


_______________________________________________
micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general
_______________________________________________
micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general


_______________________________________________
micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general
Reply | Threaded
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|

Re: Micro-manager and arduino

Quiroz1
Awesome, thanks for the info! I will look into this. 

Thanks,
Cindy

On Wed, Apr 1, 2020 at 12:39 PM Rusty Nicovich <[hidden email]> 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 <[hidden email]> wrote:
Hello,

In the link I provided you I wanted you to see this image, specifically the colors of the pins.

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

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 <[hidden email]> 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 <[hidden email]> 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
 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 <[hidden email]> 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  <[hidden email]>


_______________________________________________
micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general
_______________________________________________
micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general


_______________________________________________
micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general