are algorithms supported in uManager?

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are algorithms supported in uManager?

Micro-Manager mailing list

Hi All,

 

We upgrade our existing system and try to estimate which approach would have minimum issues. The current system is implemented in LabVIEW and doesn’t have any deal with images. We are looking on uManager and MetaMorph packages as well as LabVIEW with NI Vision Development library.

uManager. We don’t have real experience with  uManager. First of all, we found that uManager is compatibly with existing equipment (except NI USB device). Now we look that uManager has some algorithms. Here is list of algorithms which we need:

  1. Alignment camera image (pixel) with X-Y stage position.
  2. Create single image from multiply adjusted images maybe with different camera focuses
  3. Subtract image background
  4. Find features (biological cell) based X-Y dimensions
  5. Apply intensity threshold on features
  6. Find feature centers
  7. Apply filters on features based on average intensity, total intensity, centroid X, centroid Y, orientation, shape factor, length, width, etc.
  8. Convert image center coordinates to X-Y stage position

Also we know that uManager supports DI signal but we don’t know that uManager supports with external synchronization. Can uManager create and process event based on DI signal?

 

Couple words

  • MetaMorph: MetaMorph supports all algorithms but it is not free, doesn’t support some equipment, doesn’t support event. We don’t  have experience with MetaMorph.
  • LabVIEW: we have experience with LabVIEW but don’t have experience with NI Vision Development library. Our equipment works with LabVIEW or we know how to connect. We will get the best synchronization (=performance). We look through NI Vision Development library but are not sure that all algorithms are supported.

 

Any thoughts and comments are welcome!

Thanks, Andrey.

 



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Re: are algorithms supported in uManager?

Peter Haub
Hi Andrey,

my summary answer: YES - you can go for µManager.
( .. even if some of your questions are not 100% clear to me. See comments below.)

"Give it a try"

If your hardware is supported by µManager and if your are familiar with ImageJ/FIJI then you should definitely go for it.
1) Simply install µManager
2) Setup / configure your system (see may take some time if your hardware is exotic)
3) Start working ...

Regards
Peter



On 30.01.2020 00:24, Liyu, Andrey V via micro-manager-general wrote:
Hi All,

We upgrade our existing system and try to estimate which approach would have minimum issues. The current system is implemented in LabVIEW and doesn't have any deal with images. We are looking on uManager and MetaMorph packages as well as LabVIEW with NI Vision Development library.
uManager. We don't have real experience with  uManager. First of all, we found that uManager is compatibly with existing equipment (except NI USB device). Now we look that uManager has some algorithms. Here is list of algorithms which we need:

  1.  Alignment camera image (pixel) with X-Y stage position.
=> µManager moves a motorized stage to user-defined positions and capture images at those positions
(Does that answer your question?)
  2.  Create single image from multiply adjusted images maybe with different camera focuses
What does that mean?
µManager captures images e.g. on user defined position lists, where every position is defined by x,y and z. So you can captured images at certain positions with certain focus positions. (!! if you have motorized stage and microscope)
(Does that answer your question?)
  3.  Subtract image background
yes
  4.  Find features (biological cell) based X-Y dimensions
Image processing can be performed in ImageJ/FIJI due to the close relation of µManager and IJ.
Check if you can do your feature analysis in ImageJ. (Pretty sure you can.)

  5.  Apply intensity threshold on features
see 4.
  6.  Find feature centers
see 4.
  7.  Apply filters on features based on average intensity, total intensity, centroid X, centroid Y, orientation, shape factor, length, width, etc.
see 4
  8.  Convert image center coordinates to X-Y stage position
µManager stored the X-Y stage position in the image metadata. So you can transform image coordinates into stage coordinates.
Also we know that uManager supports DI signal but we don't know that uManager supports with external synchronization. Can uManager create and process event based on DI signal?
".. Micro-Magellan plugin to listen to commands on a port .."
(see µManager mailing list, subject: Starting MDA from external software)



Couple words

  *   MetaMorph: MetaMorph supports all algorithms but it is not free, doesn't support some equipment, doesn't support event. We don't  have experience with MetaMorph.
  *   LabVIEW: we have experience with LabVIEW but don't have experience with NI Vision Development library. Our equipment works with LabVIEW or we know how to connect. We will get the best synchronization (=performance). We look through NI Vision Development library but are not sure that all algorithms are supported.

Any thoughts and comments are welcome!
Thanks, Andrey.




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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: are algorithms supported in uManager?

PAVAK SHAH-4
In reply to this post by Micro-Manager mailing list
Hi Andrey,

Micro-Manager can support all of this, but there aren't pre-defined "modules" for many aspects. You generally have three ways of implementing features like this: as beanshell scripts (using Java) in the micro-manager GUI or by running micro-manager in MATLAB and controlling aspects of the acquisition and image analysis there. You can write scripts that are responsive to external signals as well. To get started on seeing how to approach tasks like this, the best place to start is probably the programming guide:


Best,
Pavak

On Wed, Jan 29, 2020 at 3:25 PM Liyu, Andrey V via micro-manager-general <[hidden email]> wrote:

Hi All,

 

We upgrade our existing system and try to estimate which approach would have minimum issues. The current system is implemented in LabVIEW and doesn’t have any deal with images. We are looking on uManager and MetaMorph packages as well as LabVIEW with NI Vision Development library.

uManager. We don’t have real experience with  uManager. First of all, we found that uManager is compatibly with existing equipment (except NI USB device). Now we look that uManager has some algorithms. Here is list of algorithms which we need:

  1. Alignment camera image (pixel) with X-Y stage position.
  2. Create single image from multiply adjusted images maybe with different camera focuses
  3. Subtract image background
  4. Find features (biological cell) based X-Y dimensions
  5. Apply intensity threshold on features
  6. Find feature centers
  7. Apply filters on features based on average intensity, total intensity, centroid X, centroid Y, orientation, shape factor, length, width, etc.
  8. Convert image center coordinates to X-Y stage position

Also we know that uManager supports DI signal but we don’t know that uManager supports with external synchronization. Can uManager create and process event based on DI signal?

 

Couple words

  • MetaMorph: MetaMorph supports all algorithms but it is not free, doesn’t support some equipment, doesn’t support event. We don’t  have experience with MetaMorph.
  • LabVIEW: we have experience with LabVIEW but don’t have experience with NI Vision Development library. Our equipment works with LabVIEW or we know how to connect. We will get the best synchronization (=performance). We look through NI Vision Development library but are not sure that all algorithms are supported.

 

Any thoughts and comments are welcome!

Thanks, Andrey.

 

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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: are algorithms supported in uManager?

Micro-Manager mailing list
In reply to this post by Peter Haub

Hi Peter,

 

Thank you very much for answers, especially, about ImageJ. We will look ImageJ and there are colleagues who use ImageJ constantly.

 

About points 1,  2 and 8 but first of all our goal is to get list of cell center and later fire laser into centers. Assumable, we are talking about ~1 um accuracy.

  1. My understanding that camera image and chip (is moved by XY stages) X and Y axis are not parallel. Also pixel size depends of focus. Finally, I wouldn’t be surprised if corner pixel will occupy more space on chip than center pixel. So we need calibrate.
  2. One image doesn’t cover whole sample. We need to make multiply real images and create single image.

8.    Conversation from single image XY pixel to real XY stage positions could be tricky.

 

Thanks, Andrey.

 

From: Peter Haub <[hidden email]>
Sent: Thursday, January 30, 2020 5:34 AM
To: [hidden email]
Subject: Re: [micro-manager-general] are algorithms supported in uManager?

 

Hi Andrey,

my summary answer: YES - you can go for µManager.
( .. even if some of your questions are not 100% clear to me. See comments below.)

"Give it a try"

If your hardware is supported by µManager and if your are familiar with ImageJ/FIJI then you should definitely go for it.
1) Simply install µManager
2) Setup / configure your system (see may take some time if your hardware is exotic)
3) Start working ...

Regards
Peter


On 30.01.2020 00:24, Liyu, Andrey V via micro-manager-general wrote:

Hi All,
 
We upgrade our existing system and try to estimate which approach would have minimum issues. The current system is implemented in LabVIEW and doesn't have any deal with images. We are looking on uManager and MetaMorph packages as well as LabVIEW with NI Vision Development library.
uManager. We don't have real experience with  uManager. First of all, we found that uManager is compatibly with existing equipment (except NI USB device). Now we look that uManager has some algorithms. Here is list of algorithms which we need:
 
  1.  Alignment camera image (pixel) with X-Y stage position.

=> µManager moves a motorized stage to user-defined positions and capture images at those positions
(Does that answer your question?)

 
  2.  Create single image from multiply adjusted images maybe with different camera focuses

What does that mean?
µManager captures images e.g. on user defined position lists, where every position is defined by x,y and z. So you can captured images at certain positions with certain focus positions. (!! if you have motorized stage and microscope)
(Does that answer your question?)

 
  3.  Subtract image background

yes

  4.  Find features (biological cell) based X-Y dimensions

Image processing can be performed in ImageJ/FIJI due to the close relation of µManager and IJ.
Check if you can do your feature analysis in ImageJ. (Pretty sure you can.)


 
  5.  Apply intensity threshold on features

see 4.

 
  6.  Find feature centers

see 4.

 
  7.  Apply filters on features based on average intensity, total intensity, centroid X, centroid Y, orientation, shape factor, length, width, etc.

see 4

 
  8.  Convert image center coordinates to X-Y stage position

µManager stored the X-Y stage position in the image metadata. So you can transform image coordinates into stage coordinates.

 
Also we know that uManager supports DI signal but we don't know that uManager supports with external synchronization. Can uManager create and process event based on DI signal?

".. Micro-Magellan plugin to listen to commands on a port .."
(see µManager mailing list, subject: Starting MDA from external software)

 
 
 
 
Couple words
 
  *   MetaMorph: MetaMorph supports all algorithms but it is not free, doesn't support some equipment, doesn't support event. We don't  have experience with MetaMorph.
  *   LabVIEW: we have experience with LabVIEW but don't have experience with NI Vision Development library. Our equipment works with LabVIEW or we know how to connect. We will get the best synchronization (=performance). We look through NI Vision Development library but are not sure that all algorithms are supported.
 
Any thoughts and comments are welcome!
Thanks, Andrey.
 
 




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

 



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