3D ROI Manager - Upper limit to number of ROIs?

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3D ROI Manager - Upper limit to number of ROIs?

Sho Fujisawa
Hi -

I'm trying to count the number of cells in 3D using 3D ROI Manager. Images are well segmented, and with a releatively small stack, "Add Image" function works well.

But with a stack that is estimated to have about 30,000 cells (according to 2D analysis of projection), "Add Image" doesn't do anything.

Is there an upper limit to the number of ROIs 3D manager can hold?

Sho Fujisawa
Senior Digital Microscopist
Molecular Cytology Core Facility
Memorial Sloan-Kettering Cancer Center
417 E68th St. ZRC-1840
New York, NY 10065
646-888-2186


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Re: 3D ROI Manager - Upper limit to number of ROIs?

Thomas Boudier-4
Hi,

Actually there is no limit on the number of objects 3D Roi Manager can
handle, however the function "add image" may take quite long to detect
all the cells.

There maybe also a problem of memory as 3D manger may require twice the
size of the image to store the objects.

I did not really investigate the limitations for 3D roi manager but if
you can provide a sample stack I will be happy to test it.

Best,

Thomas


On 12/09/2017 02:22, Sho Fujisawa wrote:

> Hi -
>
> I'm trying to count the number of cells in 3D using 3D ROI Manager. Images are well segmented, and with a releatively small stack, "Add Image" function works well.
>
> But with a stack that is estimated to have about 30,000 cells (according to 2D analysis of projection), "Add Image" doesn't do anything.
>
> Is there an upper limit to the number of ROIs 3D manager can hold?
>
> Sho Fujisawa
> Senior Digital Microscopist
> Molecular Cytology Core Facility
> Memorial Sloan-Kettering Cancer Center
> 417 E68th St. ZRC-1840
> New York, NY 10065
> 646-888-2186
>
>
> =====================================================================
>
>       Please note that this e-mail and any files transmitted from
>       Memorial Sloan Kettering Cancer Center 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.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>

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  /***************************************************************/
       Thomas Boudier, Associate Professor, UPMC,
       Universit√© Pierre et Marie Curie, Paris, France.
       BioInformatics Institute (BII)/IPAL, Singapore.
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Re: 3D ROI Manager - Upper limit to number of ROIs?

Sho Fujisawa
Thomas -

Gotcha, thanks for the info. I'll test it on the best computer we got.
I'll also send you a separate email with the stack.

Sho Fujisawa
Molecular Cytology Core Facility
Memorial Sloan-Kettering Cancer Center
415 E. 68th St. Z-1840
New York, NY 10065
(646) 888-2186
________________________________________
From: Thomas Boudier [[hidden email]]
Sent: Tuesday, September 12, 2017 2:38 AM
To: [hidden email]
Subject: [EXTERNAL] Re: 3D ROI Manager - Upper limit to number of ROIs?

*** ATTENTION: If you do not recognize this external sender ("Thomas Boudier" <[hidden email]>), do not open any links or attachments in this message. If you believe this email to be malicious, please contact the MSK Information Security Office. ***

Hi,

Actually there is no limit on the number of objects 3D Roi Manager can
handle, however the function "add image" may take quite long to detect
all the cells.

There maybe also a problem of memory as 3D manger may require twice the
size of the image to store the objects.

I did not really investigate the limitations for 3D roi manager but if
you can provide a sample stack I will be happy to test it.

Best,

Thomas


On 12/09/2017 02:22, Sho Fujisawa wrote:

> Hi -
>
> I'm trying to count the number of cells in 3D using 3D ROI Manager. Images are well segmented, and with a releatively small stack, "Add Image" function works well.
>
> But with a stack that is estimated to have about 30,000 cells (according to 2D analysis of projection), "Add Image" doesn't do anything.
>
> Is there an upper limit to the number of ROIs 3D manager can hold?
>
> Sho Fujisawa
> Senior Digital Microscopist
> Molecular Cytology Core Facility
> Memorial Sloan-Kettering Cancer Center
> 417 E68th St. ZRC-1840
> New York, NY 10065
> 646-888-2186
>
>
> =====================================================================
>
>       Please note that this e-mail and any files transmitted from
>       Memorial Sloan Kettering Cancer Center 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.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>

--
  /***************************************************************/
       Thomas Boudier, Associate Professor, UPMC,
       Universit√© Pierre et Marie Curie, Paris, France.
       BioInformatics Institute (BII)/IPAL, Singapore.
/**************************************************************/

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
=====================================================================

     Please note that this e-mail and any files transmitted from
     Memorial Sloan Kettering Cancer Center 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.

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html