3D analysis problem
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Hi, Does anyone have experience with 3D constructor in image pro plus? I am trying to do volume measurments on a complex dataset. 100mb = original size of the z stack with approx 40 z slices at 1024 resolution. I have 6 gig of RAM and a 512MB video gaming card of high spec plus and 80gig hard drive. I can reconstruct surface areas etc and the volume but when going to measure/count option the 3D volumes the software says I don't have enough memory. This is with 3x3x1 subsampling and resizing it down to 512x512? The volume we are trying to measure is probably half of the volume but complex in structure, if we subsample too much further we get too much triangulation of the data. Our IT staff can't identify which memory it doesn't have access to. Any ideas? Liz DISCLAIMER: |
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Hi Elizabeth,
It might not be what you are looking for but with ImageJ you could use the "Object counter 3D" plugin to get the volume of your structure. By the numbers I get I think the volume is in voxel but it is easy to convert. The plugins use quite a lot of memory but I can process a 500Mb z stack easily with 8Gig of ram. Gabriel Elizabeth Nickless wrote: > Hi, > > Does anyone have experience with 3D constructor in image pro plus? > > I am trying to do volume measurments on a complex dataset. 100mb = > original size of the z stack with approx 40 z slices at 1024 resolution. > > I have 6 gig of RAM and a 512MB video gaming card of high spec plus and > 80gig hard drive. > > I can reconstruct surface areas etc and the volume but when going to > measure/count option the 3D volumes the software says I don't have > enough memory. This is with 3x3x1 subsampling and resizing it down to > 512x512? > > The volume we are trying to measure is probably half of the volume but > complex in structure, if we subsample too much further we get too much > triangulation of the data. > > Our IT staff can't identify which memory it doesn't have access to. > > Any ideas? > > Liz > > > > > DISCLAIMER: > This email contains confidential information and may be legally > privileged. If you are not the intended recipient or have received this > email in error, please notify the sender immediately and destroy this email. > You may not use, disclose or copy this email or its attachments in any way. > Any opinions expressed in this email are those of the author and are not > necessarily those of the Fonterra Co-operative Group. > http://www.fonterra.com/ > |
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In reply to this post by Elizabeth Nickless
Hi Liz,
Not sure what the source of your problem is. However, we had similar issues with Volocity when using classifiers to find, count and measure objects. We figured that in noisy images, single "hot" pixels will be identified as objects, and in large data sets there can be tens of thousands of those, or more. Eventually, the software would crash trying to generate a list. We typically prevent this from happening by applying a smoothing filter that gets rid of those pixels before we start processing the stacks. There is often also an option to filter results by excluding small objects, but the utility of this filter may depend on whether the software finds all objects first, and then discards those that do not pass the test, or whether it gets rid of them as it goes. In the first case, it will not solve the out of memory issue, but in the second case, it might. Again, I don't know if this has anything to do with your problem, but may be worth a try. Julio -- Julio Vazquez, Fred Hutchinson Cancer Research Center Seattle, WA 98109-1024 On Dec 11, 2008, at 3:18 PM, Elizabeth Nickless wrote:
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In reply to this post by Elizabeth Nickless
What version of Image Pro are you using? It seems
from Media Cy's website that you'll need at least version 6.2 for 64 bit
support. Older versions apparently don't support 64 bit processing, and
thus won't support more than 4 gb of RAM. I'm assuming you're using Vista
or XP x64, otherwise Windows itself will ignore anything more than 4 gb
(actually, it will only recognize somewhere around 3 gb, since your 512 mb VRAM
counts towards the 4 gb limit, as does memory used by the system for I/O
functions).
Scott Turner From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Elizabeth Nickless Sent: Thursday, December 11, 2008 03:19 PM To: [hidden email] Subject: 3D analysis problem Hi, Does anyone have experience with 3D constructor in image pro plus? I am trying to do volume measurments on a complex dataset. 100mb = original size of the z stack with approx 40 z slices at 1024 resolution. I have 6 gig of RAM and a 512MB video gaming card of high spec plus and 80gig hard drive. I can reconstruct surface areas etc and the volume but when going to measure/count option the 3D volumes the software says I don't have enough memory. This is with 3x3x1 subsampling and resizing it down to 512x512? The volume we are trying to measure is probably half of the volume but complex in structure, if we subsample too much further we get too much triangulation of the data. Our IT staff can't identify which memory it doesn't have access to. Any ideas? Liz DISCLAIMER: ********************************************************************* This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited -- Please immediately and permanently delete. |
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In reply to this post by Elizabeth Nickless
Hi Elizabeth,
3D Constructor is a 32-bit application and can use maximum 3GB of RAM (if you enable /3G flag, as per WinXP32) . If the surface is complex it requires memory for triangulation; when you enable Count it will require even more for segmentation and measurement data. If your samples are large, I would recommend using an AOIs to define area of interest on the image which you are interested to measure or use higher sub-sampling. Using AOIs you can measure the whole sample by blocks and then get total statistics in the Data Collector. Best regards, Yuri Gaidoukevitch Media Cybernetics |
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In reply to this post by Turner, Scott
We have version 6.2 and running XP not sure about the
64bit? Will check this out with our IT though we have tried the software on a
64bit machine elsewhere without much improvement.
RE other comments on list we do smooth and filter our
images first.and adjust background to zero ..so we can rule out odd pixels and
noise. We have had a bit of improvement by changing the software that talks to
the video card.
Will check out other issues raised
THanks
Liz Nickless Microscopy and Imaging
Centre From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Turner, Scott Sent: Friday, 12 December 2008 2:19 p.m. To: [hidden email] Subject: Re: 3D analysis problem What version of Image Pro are you using? It seems
from Media Cy's website that you'll need at least version 6.2 for 64 bit
support. Older versions apparently don't support 64 bit processing, and
thus won't support more than 4 gb of RAM. I'm assuming you're using Vista
or XP x64, otherwise Windows itself will ignore anything more than 4 gb
(actually, it will only recognize somewhere around 3 gb, since your 512 mb VRAM
counts towards the 4 gb limit, as does memory used by the system for I/O
functions).
Scott Turner From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Elizabeth Nickless Sent: Thursday, December 11, 2008 03:19 PM To: [hidden email] Subject: 3D analysis problem Hi, Does anyone have experience with 3D constructor in image pro plus? I am trying to do volume measurments on a complex dataset. 100mb = original size of the z stack with approx 40 z slices at 1024 resolution. I have 6 gig of RAM and a 512MB video gaming card of high spec plus and 80gig hard drive. I can reconstruct surface areas etc and the volume but when going to measure/count option the 3D volumes the software says I don't have enough memory. This is with 3x3x1 subsampling and resizing it down to 512x512? The volume we are trying to measure is probably half of the volume but complex in structure, if we subsample too much further we get too much triangulation of the data. Our IT staff can't identify which memory it doesn't have access to. Any ideas? Liz DISCLAIMER: ********************************************************************* This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited -- Please immediately and permanently delete. DISCLAIMER: |
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