question about xy stage scan and acquistion

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question about xy stage scan and acquistion

JIAHUI HUANG
Hi Mircomanager team,

I'm going to purchase a Ludl or Prior xy stage compatible with micromanager software. 

What I want to do is to scan the xy stage by the adjustable step size (the smallest step size depends on the specification of the stage) and record the fluorescence intensity in a certain amount of exposure time at each scanning step. After scanning, I would expect to get an intensity map (z-axis is intensity, xy-axes are position). Then I want to move the stage to a certain point on that map. And maybe analysis the spectrum or other things at that point.

Would your software already have function/control panel to do that or I need some extra programming/modification of the software? I see the software has multidimensional acquisition, tile scan, and positioning functions. But I'm new to microscope and scanning staff. So I would like to direct send my question to you.

Thanks,
Jiahui


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Re: question about xy stage scan and acquistion

JonD
Administrator
Hello Jiahui,


JIAHUI HUANG wrote

> What I want to do is to scan the xy stage by the adjustable step size (the
> smallest step size depends on the specification of the stage) and record
> the fluorescence intensity in a certain amount of exposure time at each
> scanning step. After scanning, I would expect to get an intensity map
> (z-axis is intensity, xy-axes are position). Then I want to move the stage
> to a certain point on that map. And maybe analysis the spectrum or other
> things at that point.
>
> Would your software already have function/control panel to do that or I
> need some extra programming/modification of the software? I see the
> software has multidimensional acquisition, tile scan, and positioning
> functions. But I'm new to microscope and scanning staff. So I would like
> to
> direct send my question to you.

A few thoughts about your proposal:

1. Just because the stage has a particular step size doesn't mean that it
can move in that increment accurately.  If your step size is 10um I'd
believe it, but not 10nm for a mm-travel stage.  The units used internally
may have more precision than you can expect in practice.

2. MM typically is used with cameras but it sounds like you have a point
detector and want to build up an image based on multiple readings from your
point detector.  Think about how you will access the data from your point
detector in MM.  If your point detector appears as a 1-pixel camera device
in MM then I think you can use the MDA and build up the image
post-acquisition.  An alternative is to write a device adapter that acts as
a camera and returns an image that is built up point by point by scanning
the sample.  Or another alternative is to use a software like ScanImage that
is designed for building up images from a scanned point detector.

3 Consider scanning the stage slowly but continuously, especially if you
care about throughput.  Not sure about other makes of stages but ASI stages
do this well with excellent positioning (i.e. the scan is very uniform with
hardware triggering for synchronization so you always know where you are)
and have special commands for doing raster and serpentine scans like this.

-------------------------------------------
Jon Daniels
Applied Scientific Instrumentation
29391 West Enid Rd, Eugene, OR 97402
Phone: (541) 461-8181 x118
-------------------------------------------





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Re: question about xy stage scan and acquistion

Carol Heckman

Jiahui,

It's not a problem.  You can get increments even below 1 nm with PI stages.  Then vibration becomes a problem.

Carol Hecman




From: JonD <[hidden email]>
Sent: Friday, October 26, 2018 9:33 AM
To: [hidden email]
Subject: Re: [micro-manager-general] question about xy stage scan and acquistion
 
Hello Jiahui,


JIAHUI HUANG wrote
> What I want to do is to scan the xy stage by the adjustable step size (the
> smallest step size depends on the specification of the stage) and record
> the fluorescence intensity in a certain amount of exposure time at each
> scanning step. After scanning, I would expect to get an intensity map
> (z-axis is intensity, xy-axes are position). Then I want to move the stage
> to a certain point on that map. And maybe analysis the spectrum or other
> things at that point.
>
> Would your software already have function/control panel to do that or I
> need some extra programming/modification of the software? I see the
> software has multidimensional acquisition, tile scan, and positioning
> functions. But I'm new to microscope and scanning staff. So I would like
> to
> direct send my question to you.

A few thoughts about your proposal:

1. Just because the stage has a particular step size doesn't mean that it
can move in that increment accurately.  If your step size is 10um I'd
believe it, but not 10nm for a mm-travel stage.  The units used internally
may have more precision than you can expect in practice.

2. MM typically is used with cameras but it sounds like you have a point
detector and want to build up an image based on multiple readings from your
point detector.  Think about how you will access the data from your point
detector in MM.  If your point detector appears as a 1-pixel camera device
in MM then I think you can use the MDA and build up the image
post-acquisition.  An alternative is to write a device adapter that acts as
a camera and returns an image that is built up point by point by scanning
the sample.  Or another alternative is to use a software like ScanImage that
is designed for building up images from a scanned point detector.

3 Consider scanning the stage slowly but continuously, especially if you
care about throughput.  Not sure about other makes of stages but ASI stages
do this well with excellent positioning (i.e. the scan is very uniform with
hardware triggering for synchronization so you always know where you are)
and have special commands for doing raster and serpentine scans like this.

-------------------------------------------
Jon Daniels
Applied Scientific Instrumentation
29391 West Enid Rd, Eugene, OR 97402
Phone: (541) 461-8181 x118
-------------------------------------------





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