Camera issue

[Romin, Yevgeniy/Sloan Kettering Institute]

Dear List

 

We are having a small problem with our EM CCD camera that is attached to a live-imaging spinning disk Confocal microscope.  It seems that the camera chip size and the optical path dimensions are not perfectly matched, so the image on the screen has two black stripes on two sides of the image.  One thing we thought of trying is to put some sort of an optivar lens in the path, but that would cut down the viewing field size on all 4 sides, while only 2 are currently the problem.  Another idea is to draw a region in the viewing field excluding the black stripes and have only that field be shown after acquisition.  This is done using Metamorph, which is the acquisition software on that particular system.  I was wondering if anybody else ran into similar problems and whether there are some solutions that we haven’t thought of yet.

 

Thanks very much in advance to everybody

 

---------------------------------------------------

Yevgeniy Romin

 

Digital Microscopist

Memorial Sloan-Kettering Cancer Center

Molecular Cytology Core Facility

1275 York Ave. Box 333

New York, NY 10065

Tel.[phone]

Fax. [phone]

---------------------------------------------------

 

 
     =====================================================================
     
     Please note that this e-mail and any files transmitted with it may be 
     privileged, confidential, and protected from disclosure under 
     applicable law. If the reader of this message is not the intended 
     recipient, or an employee or agent responsible for delivering this 
     message to the intended recipient, you are hereby notified that any 
     reading, dissemination, distribution, copying, or other use of this 
     communication or any of its attachments is strictly prohibited.  If 
     you have received this communication in error, please notify the 
     sender immediately by replying to this message and deleting this 
     message, any attachments, and all copies and backups from your 
     computer.

[John Oreopoulos]

<base href="x-msg://218/">Which EMCCD camera are you using Yevgeniy? I could be wrong, but I thought all current EMCCD chips were square (not including the frame transfer portion) with square pixels. How many pixels actually appear in the software (512x512? Or is it a rectangular image with uneven pixel dimensions to start with?)

I think your better option is the second one you mentioned, just cropping out the black regions of the image (but this should be indicated to reviewers in any paper manuscripts that use these images). If you try magnifying the image symmetrically, it is as you said, you'll be losing useful imaging regions and also the image intensities will be lower (since you'll be spreading less light over the same pixel areas).

Did the camera you're using come with the spinning disk confocal microscope? I've never heard of a system where this was a problem and it sounds more like a design flaw if it came that way.

Perhaps there is something in the light path blocking the image? Are the edges of the black bars sharp or blurred. If they're blurred, then this could indicate a blockage somewhere in the light path (well, if they're sharp too, that wouldn't exclude the possibility of a blockage either, but it's less likely).

John Oreopoulos

On 2010-06-25, at 9:42 AM, Yevgeniy Romin wrote:

Dear List

 

We are having a small problem with our EM CCD camera that is attached to a live-imaging spinning disk Confocal microscope.  It seems that the camera chip size and the optical path dimensions are not perfectly matched, so the image on the screen has two black stripes on two sides of the image.  One thing we thought of trying is to put some sort of an optivar lens in the path, but that would cut down the viewing field size on all 4 sides, while only 2 are currently the problem.  Another idea is to draw a region in the viewing field excluding the black stripes and have only that field be shown after acquisition.  This is done using Metamorph, which is the acquisition software on that particular system.  I was wondering if anybody else ran into similar problems and whether there are some solutions that we haven’t thought of yet.

 

Thanks very much in advance to everybody

 

---------------------------------------------------

Yevgeniy Romin

 

Digital Microscopist

Memorial Sloan-Kettering Cancer Center

Molecular Cytology Core Facility

1275 York Ave. Box 333

New York, NY 10065

Tel.[phone]

Fax. [phone]

---------------------------------------------------

 

 
     =====================================================================
     
     Please note that this e-mail and any files transmitted with it may be 
     privileged, confidential, and protected from disclosure under 
     applicable law. If the reader of this message is not the intended 
     recipient, or an employee or agent responsible for delivering this 
     message to the intended recipient, you are hereby notified that any 
     reading, dissemination, distribution, copying, or other use of this 
     communication or any of its attachments is strictly prohibited.  If 
     you have received this communication in error, please notify the 
     sender immediately by replying to this message and deleting this 
     message, any attachments, and all copies and backups from your 
     computer.

[Goodhouse, Joseph G.]

You can adjust the read out area of the camera to get rid of this.  Go to camera read out and adjust left right, and top bottom.

 

Joe Goodhouse
Confocal Core Lab Manager
Dept. of Molecular Biology
Princeton University

Washington Road

Princeton, NJ. 08544-1014
609-258-5432

Visit us at http://www.molbio1.princeton.edu/facility/confocal/

 

From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Yevgeniy Romin
Sent: Friday, June 25, 2010 9:42 AM
To: [hidden email]
Subject: Camera issue

 

Dear List

 

We are having a small problem with our EM CCD camera that is attached to a live-imaging spinning disk Confocal microscope.  It seems that the camera chip size and the optical path dimensions are not perfectly matched, so the image on the screen has two black stripes on two sides of the image.  One thing we thought of trying is to put some sort of an optivar lens in the path, but that would cut down the viewing field size on all 4 sides, while only 2 are currently the problem.  Another idea is to draw a region in the viewing field excluding the black stripes and have only that field be shown after acquisition.  This is done using Metamorph, which is the acquisition software on that particular system.  I was wondering if anybody else ran into similar problems and whether there are some solutions that we haven’t thought of yet.

 

Thanks very much in advance to everybody

 

---------------------------------------------------

Yevgeniy Romin

 

Digital Microscopist

Memorial Sloan-Kettering Cancer Center

Molecular Cytology Core Facility

1275 York Ave. Box 333

New York, NY 10065

Tel.[phone]

Fax. [phone]

---------------------------------------------------

 

     =====================================================================

     Please note that this e-mail and any files transmitted with it may be 

     privileged, confidential, and protected from disclosure under 

     applicable law. If the reader of this message is not the intended 

     recipient, or an employee or agent responsible for delivering this 

     message to the intended recipient, you are hereby notified that any 

     reading, dissemination, distribution, copying, or other use of this 

     communication or any of its attachments is strictly prohibited.  If 

     you have received this communication in error, please notify the 

     sender immediately by replying to this message and deleting this 

     message, any attachments, and all copies and backups from your 

     computer.

[Rietdorf, Jens]

Dear Yevgeny,

 

for use with the Yokogawa unit you need to adapt the square size of the CCD sensor to the non-square format of the Yokogawa scan head output. We use a 1.5x c-mount adapter to fill the entire camera chip. 16micron pixel size found in some EMCCD camera variants, backprojected into the object plane without further demagnification results in undersampling for virtually all standard objectives on the market. We use optovars to address this issue, which is further complicated because the Yokogawa unit only performs well for a certain magnifiation-NA ratio.

 

Dear All,

 

has anybody tried the new sCMOS cameras on a spinning disc and compared to EMCCD?

 

Thanks & best wishes, jens

 

 

From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Yevgeniy Romin
Sent: Friday, June 25, 2010 15:42 PM
To: [hidden email]
Subject: Camera issue

 

Dear List

 

We are having a small problem with our EM CCD camera that is attached to a live-imaging spinning disk Confocal microscope.  It seems that the camera chip size and the optical path dimensions are not perfectly matched,

[Emmanuel Gustin]

<base href="x-msg://218/">

 

Of course it depends on the type of camera, but you may be able to instruct the firmware of the camera to read out only a selection of rows or columns. A good study of the manual of your camera should provide this information. Unfortunately, the low-level instruction sets are often a bit arcane, so it is easiest to use whatever configuration software was available with the camera. To make it work, you also have to tell your frame grabber (if any) and acquisition software that they should expect a reduced image size, or you are likely to see these areas filled with pseudo-random bytes.

 

The advantage of not reading out the unwanted pixels from the camera chip, is that you save the time otherwise spent on amplifying and digitizing these pixels and transmitting them to the computer. For a live-imaging systems, that may be worth the effort.

 

Best Regards,

 

Emmanuel

 

--
 Emmanuel Gustin,    Tel. [phone],    e-mail: [hidden email]     ! telephone number changed !

 

From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of John Oreopoulos
Sent: vrijdag 25 juni 2010 16:02
To: [hidden email]
Subject: Re: Camera issue

 

Which EMCCD camera are you using Yevgeniy? I could be wrong, but I thought all current EMCCD chips were square (not including the frame transfer portion) with square pixels. How many pixels actually appear in the software (512x512? Or is it a rectangular image with uneven pixel dimensions to start with?)

 

I think your better option is the second one you mentioned, just cropping out the black regions of the image (but this should be indicated to reviewers in any paper manuscripts that use these images). If you try magnifying the image symmetrically, it is as you said, you'll be losing useful imaging regions and also the image intensities will be lower (since you'll be spreading less light over the same pixel areas).

 

Did the camera you're using come with the spinning disk confocal microscope? I've never heard of a system where this was a problem and it sounds more like a design flaw if it came that way.

 

Perhaps there is something in the light path blocking the image? Are the edges of the black bars sharp or blurred. If they're blurred, then this could indicate a blockage somewhere in the light path (well, if they're sharp too, that wouldn't exclude the possibility of a blockage either, but it's less likely).

 

John Oreopoulos

 

 

On 2010-06-25, at 9:42 AM, Yevgeniy Romin wrote:

Dear List

 

We are having a small problem with our EM CCD camera that is attached to a live-imaging spinning disk Confocal microscope.  It seems that the camera chip size and the optical path dimensions are not perfectly matched, so the image on the screen has two black stripes on two sides of the image.  One thing we thought of trying is to put some sort of an optivar lens in the path, but that would cut down the viewing field size on all 4 sides, while only 2 are currently the problem.  Another idea is to draw a region in the viewing field excluding the black stripes and have only that field be shown after acquisition.  This is done using Metamorph, which is the acquisition software on that particular system.  I was wondering if anybody else ran into similar problems and whether there are some solutions that we haven’t thought of yet.

 

Thanks very much in advance to everybody

 

---------------------------------------------------

Yevgeniy Romin

 

Digital Microscopist

Memorial Sloan-Kettering Cancer Center

Molecular Cytology Core Facility

1275 York Ave. Box 333

New York, NY 10065

Tel.[phone]

Fax. [phone]

---------------------------------------------------

 

 

     =====================================================================

     Please note that this e-mail and any files transmitted with it may be 

     privileged, confidential, and protected from disclosure under 

     applicable law. If the reader of this message is not the intended 

     recipient, or an employee or agent responsible for delivering this 

     message to the intended recipient, you are hereby notified that any 

     reading, dissemination, distribution, copying, or other use of this 

     communication or any of its attachments is strictly prohibited.  If 

     you have received this communication in error, please notify the 

     sender immediately by replying to this message and deleting this 

     message, any attachments, and all copies and backups from your 

     computer.

 

 

[Ryan Geil]

As stated earlier, these black bars come from an aperture inside the
Yokogawa head that is smaller than the size of the chip on the camera.  This
will be the case with any stock Yokogawa CSU scanhead used with a 512x512
chip.  One can compensate for this by putting magnification in the path but
that is inappropriate as John points out.
One option is to crop your acquisition (also mentioned earlier).  However,
another option is to have the aperture size corrected.  Quorum Technologies
Inc. in Guelph, Ontario has extensive experience with all Yokogawa scanheads
and has a way of correcting this issue at the level of the hardware.  The
end result is maximum light to your full chip.
Ryan

On Fri, 25 Jun 2010 16:34:07 +0200, Gustin, Emmanuel [TIBBE]
<[hidden email]> wrote:

>
>
>Of course it depends on the type of camera, but you may be able to
>instruct the firmware of the camera to read out only a selection of rows
>or columns. A good study of the manual of your camera should provide
>this information. Unfortunately, the low-level instruction sets are
>often a bit arcane, so it is easiest to use whatever configuration
>software was available with the camera. To make it work, you also have
>to tell your frame grabber (if any) and acquisition software that they
>should expect a reduced image size, or you are likely to see these areas
>filled with pseudo-random bytes.
>
>
>
>The advantage of not reading out the unwanted pixels from the camera
>chip, is that you save the time otherwise spent on amplifying and
>digitizing these pixels and transmitting them to the computer. For a
>live-imaging systems, that may be worth the effort.
>
>
>
>Best Regards,
>
>
>
>Emmanuel
>
>
>
>--
> Emmanuel Gustin,    Tel. [phone],    e-mail:
>[hidden email] <mailto:[hidden email]>      ! telephone number
>changed !
>
>
>
>
>
>From: Confocal Microscopy List [mailto:[hidden email]]
>On Behalf Of John Oreopoulos
>Sent: vrijdag 25 juni 2010 16:02
>To: [hidden email]
>Subject: Re: Camera issue
>
>
>
>Which EMCCD camera are you using Yevgeniy? I could be wrong, but I
>thought all current EMCCD chips were square (not including the frame
>transfer portion) with square pixels. How many pixels actually appear in
>the software (512x512? Or is it a rectangular image with uneven pixel
>dimensions to start with?)
>
>
>
>I think your better option is the second one you mentioned, just
>cropping out the black regions of the image (but this should be
>indicated to reviewers in any paper manuscripts that use these images).
>If you try magnifying the image symmetrically, it is as you said, you'll
>be losing useful imaging regions and also the image intensities will be
>lower (since you'll be spreading less light over the same pixel areas).
>
>
>
>Did the camera you're using come with the spinning disk confocal
>microscope? I've never heard of a system where this was a problem and it
>sounds more like a design flaw if it came that way.
>
>
>
>Perhaps there is something in the light path blocking the image? Are the
>edges of the black bars sharp or blurred. If they're blurred, then this
>could indicate a blockage somewhere in the light path (well, if they're
>sharp too, that wouldn't exclude the possibility of a blockage either,
>but it's less likely).
>
>
>
>John Oreopoulos
>
>
>
>
>
>On 2010-06-25, at 9:42 AM, Yevgeniy Romin wrote:
>
>
>
>
>
>Dear List
>
>
>
>We are having a small problem with our EM CCD camera that is attached to
>a live-imaging spinning disk Confocal microscope.  It seems that the
>camera chip size and the optical path dimensions are not perfectly
>matched, so the image on the screen has two black stripes on two sides
>of the image.  One thing we thought of trying is to put some sort of an
>optivar lens in the path, but that would cut down the viewing field size
>on all 4 sides, while only 2 are currently the problem.  Another idea is
>to draw a region in the viewing field excluding the black stripes and
>have only that field be shown after acquisition.  This is done using
>Metamorph, which is the acquisition software on that particular system.
>I was wondering if anybody else ran into similar problems and whether
>there are some solutions that we haven't thought of yet.
>
>
>
>Thanks very much in advance to everybody
>
>
>
>---------------------------------------------------
>
>Yevgeniy Romin
>
>
>
>Digital Microscopist
>
>Memorial Sloan-Kettering Cancer Center
>
>Molecular Cytology Core Facility
>
>1275 York Ave. Box 333
>
>New York, NY 10065
>
>Tel.[phone]
>
>Fax. [phone]
>
>---------------------------------------------------
>
>
>
>
>
>
>
>=====================================================================
>    
>     Please note that this e-mail and any files transmitted with it may
>be
>     privileged, confidential, and protected from disclosure under
>     applicable law. If the reader of this message is not the intended
>     recipient, or an employee or agent responsible for delivering this
>     message to the intended recipient, you are hereby notified that any
>
>     reading, dissemination, distribution, copying, or other use of this
>
>     communication or any of its attachments is strictly prohibited.  If
>
>     you have received this communication in error, please notify the
>     sender immediately by replying to this message and deleting this
>     message, any attachments, and all copies and backups from your
>     computer.
>
>
>
>
>
>

[Romin, Yevgeniy/Sloan Kettering Institute]

Thank you very much for all your responses.  I am now in contact with a representative from Andor (that's the camera that we're using) and we're discussing the potential solutions.  To answer an earlier question - it is not the camera that the system came with.  It seems that the most common solution is installing a 1.2 coupler.  So we might do that or limit the acquisition field by cropping using Metamorph.

Again, thank you, everybody has been very helpful as always.

---------------------------------------------------
Yevgeniy Romin

Digital Microscopist
Memorial Sloan-Kettering Cancer Center
Molecular Cytology Core Facility
1275 York Ave. Box 333
New York, NY 10065
Tel.[phone]
Fax. [phone]
---------------------------------------------------


-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Ryan Geil
Sent: Friday, June 25, 2010 11:40 AM
To: [hidden email]
Subject: Re: Camera issue

As stated earlier, these black bars come from an aperture inside the
Yokogawa head that is smaller than the size of the chip on the camera.  This
will be the case with any stock Yokogawa CSU scanhead used with a 512x512
chip.  One can compensate for this by putting magnification in the path but
that is inappropriate as John points out.
One option is to crop your acquisition (also mentioned earlier).  However,
another option is to have the aperture size corrected.  Quorum Technologies
Inc. in Guelph, Ontario has extensive experience with all Yokogawa scanheads
and has a way of correcting this issue at the level of the hardware.  The
end result is maximum light to your full chip.
Ryan

On Fri, 25 Jun 2010 16:34:07 +0200, Gustin, Emmanuel [TIBBE]
<[hidden email]> wrote:

>
>
>Of course it depends on the type of camera, but you may be able to
>instruct the firmware of the camera to read out only a selection of rows
>or columns. A good study of the manual of your camera should provide
>this information. Unfortunately, the low-level instruction sets are
>often a bit arcane, so it is easiest to use whatever configuration
>software was available with the camera. To make it work, you also have
>to tell your frame grabber (if any) and acquisition software that they
>should expect a reduced image size, or you are likely to see these areas
>filled with pseudo-random bytes.
>
>
>
>The advantage of not reading out the unwanted pixels from the camera
>chip, is that you save the time otherwise spent on amplifying and
>digitizing these pixels and transmitting them to the computer. For a
>live-imaging systems, that may be worth the effort.
>
>
>
>Best Regards,
>
>
>
>Emmanuel
>
>
>
>--
> Emmanuel Gustin,    Tel. [phone],    e-mail:
>[hidden email] <mailto:[hidden email]>      ! telephone number
>changed !
>
>
>
>
>
>From: Confocal Microscopy List [mailto:[hidden email]]
>On Behalf Of John Oreopoulos
>Sent: vrijdag 25 juni 2010 16:02
>To: [hidden email]
>Subject: Re: Camera issue
>
>
>
>Which EMCCD camera are you using Yevgeniy? I could be wrong, but I
>thought all current EMCCD chips were square (not including the frame
>transfer portion) with square pixels. How many pixels actually appear in
>the software (512x512? Or is it a rectangular image with uneven pixel
>dimensions to start with?)
>
>
>
>I think your better option is the second one you mentioned, just
>cropping out the black regions of the image (but this should be
>indicated to reviewers in any paper manuscripts that use these images).
>If you try magnifying the image symmetrically, it is as you said, you'll
>be losing useful imaging regions and also the image intensities will be
>lower (since you'll be spreading less light over the same pixel areas).
>
>
>
>Did the camera you're using come with the spinning disk confocal
>microscope? I've never heard of a system where this was a problem and it
>sounds more like a design flaw if it came that way.
>
>
>
>Perhaps there is something in the light path blocking the image? Are the
>edges of the black bars sharp or blurred. If they're blurred, then this
>could indicate a blockage somewhere in the light path (well, if they're
>sharp too, that wouldn't exclude the possibility of a blockage either,
>but it's less likely).
>
>
>
>John Oreopoulos
>
>
>
>
>
>On 2010-06-25, at 9:42 AM, Yevgeniy Romin wrote:
>
>
>
>
>
>Dear List
>
>
>
>We are having a small problem with our EM CCD camera that is attached to
>a live-imaging spinning disk Confocal microscope.  It seems that the
>camera chip size and the optical path dimensions are not perfectly
>matched, so the image on the screen has two black stripes on two sides
>of the image.  One thing we thought of trying is to put some sort of an
>optivar lens in the path, but that would cut down the viewing field size
>on all 4 sides, while only 2 are currently the problem.  Another idea is
>to draw a region in the viewing field excluding the black stripes and
>have only that field be shown after acquisition.  This is done using
>Metamorph, which is the acquisition software on that particular system.
>I was wondering if anybody else ran into similar problems and whether
>there are some solutions that we haven't thought of yet.
>
>
>
>Thanks very much in advance to everybody
>
>
>
>---------------------------------------------------
>
>Yevgeniy Romin
>
>
>
>Digital Microscopist
>
>Memorial Sloan-Kettering Cancer Center
>
>Molecular Cytology Core Facility
>
>1275 York Ave. Box 333
>
>New York, NY 10065
>
>Tel.[phone]
>
>Fax. [phone]
>
>---------------------------------------------------
>
>
>
>
>
>
>
>=====================================================================
>
>     Please note that this e-mail and any files transmitted with it may
>be
>     privileged, confidential, and protected from disclosure under
>     applicable law. If the reader of this message is not the intended
>     recipient, or an employee or agent responsible for delivering this
>     message to the intended recipient, you are hereby notified that any
>
>     reading, dissemination, distribution, copying, or other use of this
>
>     communication or any of its attachments is strictly prohibited.  If
>
>     you have received this communication in error, please notify the
>     sender immediately by replying to this message and deleting this
>     message, any attachments, and all copies and backups from your
>     computer.
>
>
>
>
>
>

[James Pawley]

>Thank you very much for all your responses.  I am now in contact
>with a representative from Andor (that's the camera that we're
>using) and we're discussing the potential solutions.  To answer an
>earlier question - it is not the camera that the system came with.
>It seems that the most common solution is installing a 1.2 coupler.
>So we might do that or limit the acquisition field by cropping using
>Metamorph.
>
>Again, thank you, everybody has been very helpful as always.
>
>---------------------------------------------------
>Yevgeniy Romin
>
>Digital Microscopist
>Memorial Sloan-Kettering Cancer Center
>Molecular Cytology Core Facility
>1275 York Ave. Box 333
>New York, NY 10065
>Tel.[phone]
>Fax. [phone]
>---------------------------------------------------

Hi all,

Missing from this discussion so far is the name Nyquist. The primary
constraint that determines the proper magnification of the imaged
space of the Yokogawa (or any other imaging system) is not that we
can or cannot totally fill our computer screen with light, it is that
the pixels be at lease 2x smaller than the expected resolution of the
optical system at the plane of the sensor.

So if you think that your optics will produce 250 nm data (NA 1.4 in
green light) and you have large 16 micrometer pixels, as does the E2V
chip, then you need a total magnification of 200x between the object
and the CCD. I believe that I am right in saying that under these
conditions, you will be able to image only a fraction (presumably
near the centre) of the rectangular image space of the Yokogawa.
Should you decide that you want to operate at lower NA then this will
reduce your xy resolution and a proportionally lower total
magnification will be appropriate.

Should you switch to th eTI EM-CCD with 8 micrometer pixels, 100x
will be sufficient for 250 nm resolution, but the QE and noise
figures will be a bit worse.

Of course, using higher total magnification will reduce the
signal/pixel but as the BL E2V chip produces virtually no read noise,
this is no disadvantage, except that you will only cover a fraction
of the field of view.

Regards,

Jim Pawley

>
>-----Original Message-----
>From: Confocal Microscopy List
>[mailto:[hidden email]] On Behalf Of Ryan Geil
>Sent: Friday, June 25, 2010 11:40 AM
>To: [hidden email]
>Subject: Re: Camera issue
>
>As stated earlier, these black bars come from an aperture inside the
>Yokogawa head that is smaller than the size of the chip on the camera.  This
>will be the case with any stock Yokogawa CSU scanhead used with a 512x512
>chip.  One can compensate for this by putting magnification in the path but
>that is inappropriate as John points out.
>One option is to crop your acquisition (also mentioned earlier).  However,
>another option is to have the aperture size corrected.  Quorum Technologies
>Inc. in Guelph, Ontario has extensive experience with all Yokogawa scanheads
>and has a way of correcting this issue at the level of the hardware.  The
>end result is maximum light to your full chip.
>Ryan
>
>On Fri, 25 Jun 2010 16:34:07 +0200, Gustin, Emmanuel [TIBBE]
><[hidden email]> wrote:
>
>>
>>
>>Of course it depends on the type of camera, but you may be able to
>>instruct the firmware of the camera to read out only a selection of rows
>>or columns. A good study of the manual of your camera should provide
>>this information. Unfortunately, the low-level instruction sets are
>>often a bit arcane, so it is easiest to use whatever configuration
>>software was available with the camera. To make it work, you also have
>>to tell your frame grabber (if any) and acquisition software that they
>>should expect a reduced image size, or you are likely to see these areas
>>filled with pseudo-random bytes.
>>
>>
>>
>>The advantage of not reading out the unwanted pixels from the camera
>>chip, is that you save the time otherwise spent on amplifying and
>>digitizing these pixels and transmitting them to the computer. For a
>  >live-imaging systems, that may be worth the effort.
>>
>>
>>
>>Best Regards,
>>
>>
>>
>>Emmanuel
>>
>>
>>
>>--
>>  Emmanuel Gustin,    Tel. [phone],    e-mail:
>>[hidden email] <mailto:[hidden email]>      ! telephone number
>>changed !
>>
>>
>>
>>
>>
>>From: Confocal Microscopy List [mailto:[hidden email]]
>>On Behalf Of John Oreopoulos
>>Sent: vrijdag 25 juni 2010 16:02
>>To: [hidden email]
>>Subject: Re: Camera issue
>>
>>
>>
>>Which EMCCD camera are you using Yevgeniy? I could be wrong, but I
>>thought all current EMCCD chips were square (not including the frame
>>transfer portion) with square pixels. How many pixels actually appear in
>>the software (512x512? Or is it a rectangular image with uneven pixel
>>dimensions to start with?)
>>
>>
>>
>>I think your better option is the second one you mentioned, just
>>cropping out the black regions of the image (but this should be
>>indicated to reviewers in any paper manuscripts that use these images).
>>If you try magnifying the image symmetrically, it is as you said, you'll
>>be losing useful imaging regions and also the image intensities will be
>>lower (since you'll be spreading less light over the same pixel areas).
>>
>>
>>
>>Did the camera you're using come with the spinning disk confocal
>>microscope? I've never heard of a system where this was a problem and it
>>sounds more like a design flaw if it came that way.
>>
>>
>>
>>Perhaps there is something in the light path blocking the image? Are the
>>edges of the black bars sharp or blurred. If they're blurred, then this
>>could indicate a blockage somewhere in the light path (well, if they're
>>sharp too, that wouldn't exclude the possibility of a blockage either,
>>but it's less likely).
>>
>>
>>
>>John Oreopoulos
>>
>>
>>
>>
>>
>>On 2010-06-25, at 9:42 AM, Yevgeniy Romin wrote:
>>
>>
>>
>>
>>
>>Dear List
>>
>>
>>
>>We are having a small problem with our EM CCD camera that is attached to
>>a live-imaging spinning disk Confocal microscope.  It seems that the
>>camera chip size and the optical path dimensions are not perfectly
>>matched, so the image on the screen has two black stripes on two sides
>>of the image.  One thing we thought of trying is to put some sort of an
>>optivar lens in the path, but that would cut down the viewing field size
>>on all 4 sides, while only 2 are currently the problem.  Another idea is
>>to draw a region in the viewing field excluding the black stripes and
>>have only that field be shown after acquisition.  This is done using
>>Metamorph, which is the acquisition software on that particular system.
>>I was wondering if anybody else ran into similar problems and whether
>>there are some solutions that we haven't thought of yet.
>>
>>
>>
>>Thanks very much in advance to everybody
>>
>>
>>
>>---------------------------------------------------
>>
>>Yevgeniy Romin
>>
>>
>>
>>Digital Microscopist
>>
>>Memorial Sloan-Kettering Cancer Center
>>
>>Molecular Cytology Core Facility
>>
>>1275 York Ave. Box 333
>>
>>New York, NY 10065
>>
>>Tel.[phone]
>>
>>Fax. [phone]
>>
>>---------------------------------------------------
>>
>>
>>
>>
>>
>>
>>
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--
                    ****************************************
Prof. James B. Pawley,                                     Phone: [phone]
3D Microscopy of Living Cells: Summer Course   CELL: 778-318-3469
Info at: http://www.3dcourse.ubc.ca
"If it isn't diffraction, it is statistics":Microscopist's complaint, Anon.

[Jerry (Gerald) Sedgewick]

In light of the recent PPI/DPI discussion, the 1st Annual Imaging in Research Course would be an ideal way to learn methods for navigating the pdf/publication requirements.  Seats are still open.  Check the course out at http://www.imagingandanalysis.com/seminars.html...

...or read on for more information:

The "1st Annual Imaging in Research Course: Ethics, Acquisition, Post-Processing, Output and Segmenting" is being held at the University of Minnesota Continuing Education Center in Minneapolis/St. Paul, Minnesota, August 16 - 19, 2010, sponsored by the Histochemical Society and the Adobe Corporation.  Attendees can choose to attend the course for 3- or 4-days.  This workshop will educate those in science, medicine and engineering about correct techniques when acquiring, post-processing, and adjusting images for outputs; along with techniques that work for segmenting complex, biological images (for subsequent image analysis).

Other benefits of taking the course will likely result in:

Faster acceptance of submitted manuscripts
Authors better able to demonstrate outcomes to their target audience
Faster results from quantitation, with improved ability to segment desired features
Better documentation of imaging procedures
Standardization of post-processing
Learning to adjust and modify images minimally and through the objective use of numbers.

Jerry Sedgewick will present, along with invited speakers.  Jerry directed a core light microscopy and imaging facility for 15 years at the University of Minnesota, published 2 books on Photoshop and digital imaging, and his quantitative work has led to FDA approval for start up companies.

Please go to http://www.imagingandanalysis.com/seminars.html for more information.  There is a limit of 30 seats.

The cost is $590 for 3-days and $840 for 4-days, U.S. dollars. It includes lunch, beverages and snacks.  Registrations for those who received information about this course via their core facility will receive discounts.

All the best,

Jerry Sedgewick



Jerry