Memory issue
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Apologies if this has been addressed before - I searched for my issue in previous threads, but hadn't seen the specific problem I'm having anywhere. I'm trying to open a fairly large file (3 GB) which is a Z series over time with multiple stage locations totaling about 2800 images. I've opened these routinely on a mac mini running both 10.6.8 and 10.7, with the computer having 8 GB of RAM. Generally, they open in about 10 minutes.
Right now I'm working at home on a 64 bit Windows 7 machine with an intel i7 3.4 GHz processor with 16 GB of RAM on a 64 bit version of FIJI, so I would expect the files to open even faster, however this isn't happening. I haven't gotten one to open at all yet, and I've been waiting over an hour. I checked the memory and threads, and it's set to use 12000 MB of memory (so the 75% of the total memory that was recommended on the FIJI wiki) with 8 threads and the "Run garbage collector on status bar" box is checked. I have tried using less threads and less memory, but the results don't change. I am monitoring the computer's performance, and the CPU usage shifts between 12% and 15% while the memory usage is between 4.00 and 4.7 GB, generally with at least 8GB "free." Is there something I'm overlooking about changing the memory allocation? FIJI seems to ignore whatever I set. Thanks, -Andrew |
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Andrew,
I am not sure why it's loading so slow for you. Have you tried opening the images as a virtual stack? That may not be what you want but it will certainly load faster (at the cost of slower processing). Also, you might want to close ImageJ and try opening the stack again. I hope this helps a little. -Aaron On Wed, Oct 2, 2013 at 10:21 PM, Andrew Riching <[hidden email]> wrote: > Apologies if this has been addressed before - I searched for my issue in > previous threads, but hadn't seen the specific problem I'm having anywhere. > I'm trying to open a fairly large file (3 GB) which is a Z series over time > with multiple stage locations totaling about 2800 images. I've opened these > routinely on a mac mini running both 10.6.8 and 10.7, with the computer > having 8 GB of RAM. Generally, they open in about 10 minutes. > > Right now I'm working at home on a 64 bit Windows 7 machine with an intel > i7 > 3.4 GHz processor with 16 GB of RAM on a 64 bit version of FIJI, so I would > expect the files to open even faster, however this isn't happening. I > haven't gotten one to open at all yet, and I've been waiting over an hour. > I > checked the memory and threads, and it's set to use 12000 MB of memory (so > the 75% of the total memory that was recommended on the FIJI wiki) with 8 > threads and the "Run garbage collector on status bar" box is checked. I > have > tried using less threads and less memory, but the results don't change. I > am > monitoring the computer's performance, and the CPU usage shifts between 12% > and 15% while the memory usage is between 4.00 and 4.7 GB, generally with > at > least 8GB "free." > > Is there something I'm overlooking about changing the memory allocation? > FIJI seems to ignore whatever I set. > > Thanks, > -Andrew > > > > -- > View this message in context: > http://imagej.1557.x6.nabble.com/Memory-issue-tp5005018.html > Sent from the ImageJ mailing list archive at Nabble.com. > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hey all,
A short question: Does anybody know how to set up the size of "Rectanglar tool"? For instance, draw a rectangular with 500x800um in a normalized picture or even pixels in the original picture (e.g. make the square with a set size but not adjust it carefully)? Thank you very much in advance! Cheers, Hongbo On Oct 3, 2013, at 5:22 AM, Aaron Hendrickson <[hidden email]> wrote: > Andrew, > I am not sure why it's loading so slow for you. Have you tried opening the > images as a virtual stack? That may not be what you want but it will > certainly load faster (at the cost of slower processing). Also, you might > want to close ImageJ and try opening the stack again. I hope this helps a > little. > > -Aaron > > > On Wed, Oct 2, 2013 at 10:21 PM, Andrew Riching <[hidden email]> wrote: > >> Apologies if this has been addressed before - I searched for my issue in >> previous threads, but hadn't seen the specific problem I'm having anywhere. >> I'm trying to open a fairly large file (3 GB) which is a Z series over time >> with multiple stage locations totaling about 2800 images. I've opened these >> routinely on a mac mini running both 10.6.8 and 10.7, with the computer >> having 8 GB of RAM. Generally, they open in about 10 minutes. >> >> Right now I'm working at home on a 64 bit Windows 7 machine with an intel >> i7 >> 3.4 GHz processor with 16 GB of RAM on a 64 bit version of FIJI, so I would >> expect the files to open even faster, however this isn't happening. I >> haven't gotten one to open at all yet, and I've been waiting over an hour. >> I >> checked the memory and threads, and it's set to use 12000 MB of memory (so >> the 75% of the total memory that was recommended on the FIJI wiki) with 8 >> threads and the "Run garbage collector on status bar" box is checked. I >> have >> tried using less threads and less memory, but the results don't change. I >> am >> monitoring the computer's performance, and the CPU usage shifts between 12% >> and 15% while the memory usage is between 4.00 and 4.7 GB, generally with >> at >> least 8GB "free." >> >> Is there something I'm overlooking about changing the memory allocation? >> FIJI seems to ignore whatever I set. >> >> Thanks, >> -Andrew >> >> >> >> -- >> View this message in context: >> http://imagej.1557.x6.nabble.com/Memory-issue-tp5005018.html >> Sent from the ImageJ mailing list archive at Nabble.com. >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
// Spam /// Re: Rectanglar tool using
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-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512 Hello, use Edit>Selection>Specify.... You can choose between pixel and scaled units in the dialog that will be opened. Volker Hongbo Zhang: > Hey all, > > A short question: Does anybody know how to set up the size of > "Rectanglar tool"? For instance, draw a rectangular with 500x800um > in a normalized picture or even pixels in the original picture > (e.g. make the square with a set size but not adjust it > carefully)? > > Thank you very much in advance! > > Cheers, Hongbo > > > On Oct 3, 2013, at 5:22 AM, Aaron Hendrickson <[hidden email]> > wrote: > >> Andrew, I am not sure why it's loading so slow for you. Have you >> tried opening the images as a virtual stack? That may not be >> what you want but it will certainly load faster (at the cost of >> slower processing). Also, you might want to close ImageJ and >> try opening the stack again. I hope this helps a little. >> >> -Aaron >> >> >> On Wed, Oct 2, 2013 at 10:21 PM, Andrew Riching >> <[hidden email]> wrote: >> >>> Apologies if this has been addressed before - I searched for my >>> issue in previous threads, but hadn't seen the specific problem >>> I'm having anywhere. I'm trying to open a fairly large file (3 >>> GB) which is a Z series over time with multiple stage locations >>> totaling about 2800 images. I've opened these routinely on a >>> mac mini running both 10.6.8 and 10.7, with the computer having >>> 8 GB of RAM. Generally, they open in about 10 minutes. >>> >>> Right now I'm working at home on a 64 bit Windows 7 machine >>> with an intel i7 3.4 GHz processor with 16 GB of RAM on a 64 >>> bit version of FIJI, so I would expect the files to open even >>> faster, however this isn't happening. I haven't gotten one to >>> open at all yet, and I've been waiting over an hour. I checked >>> the memory and threads, and it's set to use 12000 MB of memory >>> (so the 75% of the total memory that was recommended on the >>> FIJI wiki) with 8 threads and the "Run garbage collector on >>> status bar" box is checked. I have tried using less threads and >>> less memory, but the results don't change. I am monitoring the >>> computer's performance, and the CPU usage shifts between 12% >>> and 15% while the memory usage is between 4.00 and 4.7 GB, >>> generally with at least 8GB "free." >>> >>> Is there something I'm overlooking about changing the memory >>> allocation? FIJI seems to ignore whatever I set. >>> >>> Thanks, -Andrew >>> >>> >>> >>> -- View this message in context: >>> http://imagej.1557.x6.nabble.com/Memory-issue-tp5005018.html >>> Sent from the ImageJ mailing list archive at Nabble.com. >>> >>> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html >>> >> >> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -----BEGIN PGP SIGNATURE----- iQEcBAEBCgAGBQJSTR1mAAoJENcVU956o58NedUH/30KdUSYJQuyQs22zTAIFZl2 RWEvD4ljxDfyURq918K8tuVwiTnz55TJ2F1FZA3rN6nli/2XtvvuugsKpctmY/d9 Ypu3CGVBh7g4n+N/qKxVEtq6E9UgeZL+7MJSPZNy6qRTb5TVUNuFOa2fZ5fPzl+a BFwtapwXGj4t9ig5JD0Op5H0YTo1KEp+CloTxtuJMsFr5mH8ru9sU7+kNgTMAHF6 71HTLDHghLnlKdCzr6QxOXsX1rWb8k8tlgIQyuQwviGP8vQisfsVe9nnAWIw95rU zNSzZB6uqcSpQthOf///5UxUxKl4wb52CUzFOvDT0jf+19VFhtfD2wRxmJLf4q8= =sGbP -----END PGP SIGNATURE----- -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: // Spam /// Re: Rectanglar tool using
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Thank you so much Volker!
On Oct 3, 2013, at 9:31 AM, Volker Baecker <[hidden email]> wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA512 > > Hello, > use Edit>Selection>Specify.... You can choose between pixel and scaled > units in the dialog that will be opened. > Volker > > Hongbo Zhang: >> Hey all, >> >> A short question: Does anybody know how to set up the size of >> "Rectanglar tool"? For instance, draw a rectangular with 500x800um >> in a normalized picture or even pixels in the original picture >> (e.g. make the square with a set size but not adjust it >> carefully)? >> >> Thank you very much in advance! >> >> Cheers, Hongbo >> >> >> On Oct 3, 2013, at 5:22 AM, Aaron Hendrickson <[hidden email]> >> wrote: >> >>> Andrew, I am not sure why it's loading so slow for you. Have you >>> tried opening the images as a virtual stack? That may not be >>> what you want but it will certainly load faster (at the cost of >>> slower processing). Also, you might want to close ImageJ and >>> try opening the stack again. I hope this helps a little. >>> >>> -Aaron >>> >>> >>> On Wed, Oct 2, 2013 at 10:21 PM, Andrew Riching >>> <[hidden email]> wrote: >>> >>>> Apologies if this has been addressed before - I searched for my >>>> issue in previous threads, but hadn't seen the specific problem >>>> I'm having anywhere. I'm trying to open a fairly large file (3 >>>> GB) which is a Z series over time with multiple stage locations >>>> totaling about 2800 images. I've opened these routinely on a >>>> mac mini running both 10.6.8 and 10.7, with the computer having >>>> 8 GB of RAM. Generally, they open in about 10 minutes. >>>> >>>> Right now I'm working at home on a 64 bit Windows 7 machine >>>> with an intel i7 3.4 GHz processor with 16 GB of RAM on a 64 >>>> bit version of FIJI, so I would expect the files to open even >>>> faster, however this isn't happening. I haven't gotten one to >>>> open at all yet, and I've been waiting over an hour. I checked >>>> the memory and threads, and it's set to use 12000 MB of memory >>>> (so the 75% of the total memory that was recommended on the >>>> FIJI wiki) with 8 threads and the "Run garbage collector on >>>> status bar" box is checked. I have tried using less threads and >>>> less memory, but the results don't change. I am monitoring the >>>> computer's performance, and the CPU usage shifts between 12% >>>> and 15% while the memory usage is between 4.00 and 4.7 GB, >>>> generally with at least 8GB "free." >>>> >>>> Is there something I'm overlooking about changing the memory >>>> allocation? FIJI seems to ignore whatever I set. >>>> >>>> Thanks, -Andrew >>>> >>>> >>>> >>>> -- View this message in context: >>>> http://imagej.1557.x6.nabble.com/Memory-issue-tp5005018.html >>>> Sent from the ImageJ mailing list archive at Nabble.com. >>>> >>>> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html >>>> >>> >>> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> >> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> > > -----BEGIN PGP SIGNATURE----- > > iQEcBAEBCgAGBQJSTR1mAAoJENcVU956o58NedUH/30KdUSYJQuyQs22zTAIFZl2 > RWEvD4ljxDfyURq918K8tuVwiTnz55TJ2F1FZA3rN6nli/2XtvvuugsKpctmY/d9 > Ypu3CGVBh7g4n+N/qKxVEtq6E9UgeZL+7MJSPZNy6qRTb5TVUNuFOa2fZ5fPzl+a > BFwtapwXGj4t9ig5JD0Op5H0YTo1KEp+CloTxtuJMsFr5mH8ru9sU7+kNgTMAHF6 > 71HTLDHghLnlKdCzr6QxOXsX1rWb8k8tlgIQyuQwviGP8vQisfsVe9nnAWIw95rU > zNSzZB6uqcSpQthOf///5UxUxKl4wb52CUzFOvDT0jf+19VFhtfD2wRxmJLf4q8= > =sGbP > -----END PGP SIGNATURE----- > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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In reply to this post by Andrew Riching
So I'm no programmer. But I routinely open 6-10 GB stacks with FIJI on
my computer, so it can work. You may want to check your hard drive speed. I had issues with that at one point a long time ago and needed to replace a disk. Probably not your issue, but maybe. It takes me about 5 minutes to open a stack. I'm on 64-bit linux. ImageJ 1.48d with Java 1.6.0_24 installed. 16GB of ram, but I only allocate 8277 to Image J with 4 threads. I wish I could be more help. On 10/02/2013 10:21 PM, Andrew Riching wrote: > Apologies if this has been addressed before - I searched for my issue in > previous threads, but hadn't seen the specific problem I'm having anywhere. > I'm trying to open a fairly large file (3 GB) which is a Z series over time > with multiple stage locations totaling about 2800 images. I've opened these > routinely on a mac mini running both 10.6.8 and 10.7, with the computer > having 8 GB of RAM. Generally, they open in about 10 minutes. > > Right now I'm working at home on a 64 bit Windows 7 machine with an intel i7 > 3.4 GHz processor with 16 GB of RAM on a 64 bit version of FIJI, so I would > expect the files to open even faster, however this isn't happening. I > haven't gotten one to open at all yet, and I've been waiting over an hour. I > checked the memory and threads, and it's set to use 12000 MB of memory (so > the 75% of the total memory that was recommended on the FIJI wiki) with 8 > threads and the "Run garbage collector on status bar" box is checked. I have > tried using less threads and less memory, but the results don't change. I am > monitoring the computer's performance, and the CPU usage shifts between 12% > and 15% while the memory usage is between 4.00 and 4.7 GB, generally with at > least 8GB "free." > > Is there something I'm overlooking about changing the memory allocation? > FIJI seems to ignore whatever I set. > > Thanks, > -Andrew > > > > -- > View this message in context: http://imagej.1557.x6.nabble.com/Memory-issue-tp5005018.html > Sent from the ImageJ mailing list archive at Nabble.com. > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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In reply to this post by Andrew Riching
Hi Andrew,
> I'm trying to open a fairly large file (3 GB) which is a Z series over > time with multiple stage locations totaling about 2800 images. What is the file format? Does it work if you use File > Import > Bio-Formats with the "Use virtual stack" option checked? With that option enabled, your data should open in less than 1 minute (typically less than 10 seconds). Regards, Curtis On Wed, Oct 2, 2013 at 9:21 PM, Andrew Riching <[hidden email]> wrote: > Apologies if this has been addressed before - I searched for my issue in > previous threads, but hadn't seen the specific problem I'm having anywhere. > I'm trying to open a fairly large file (3 GB) which is a Z series over time > with multiple stage locations totaling about 2800 images. I've opened these > routinely on a mac mini running both 10.6.8 and 10.7, with the computer > having 8 GB of RAM. Generally, they open in about 10 minutes. > > Right now I'm working at home on a 64 bit Windows 7 machine with an intel > i7 > 3.4 GHz processor with 16 GB of RAM on a 64 bit version of FIJI, so I would > expect the files to open even faster, however this isn't happening. I > haven't gotten one to open at all yet, and I've been waiting over an hour. > I > checked the memory and threads, and it's set to use 12000 MB of memory (so > the 75% of the total memory that was recommended on the FIJI wiki) with 8 > threads and the "Run garbage collector on status bar" box is checked. I > have > tried using less threads and less memory, but the results don't change. I > am > monitoring the computer's performance, and the CPU usage shifts between 12% > and 15% while the memory usage is between 4.00 and 4.7 GB, generally with > at > least 8GB "free." > > Is there something I'm overlooking about changing the memory allocation? > FIJI seems to ignore whatever I set. > > Thanks, > -Andrew > > > > -- > View this message in context: > http://imagej.1557.x6.nabble.com/Memory-issue-tp5005018.html > Sent from the ImageJ mailing list archive at Nabble.com. > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi Curtis,
The format is thousands of individual TIFF files compiled into a folder. I collected the images using a Prairie scope (PrairieView software), so I'm using the .XML file to open everything. I have not tried a virtual stack, but I can try that when I get home tonight. At work, I successfully opened the file on a Mac 10.6.8 machine with 8 GB of RAM and a 2 GHz dual core processor in 20 minutes. I should also note that the file is on an external harddrive. At home I was loading into a USB 3.0 port, but at work I only have USB 2.0 ports. In theory, every aspect of my home computer I would expect to outperform the lab computer as far as hardware. I should note that I have never tried to open the files on a Windows operating system (We have XP installed on our lab computers, but XP only recognizes around 3GB of RAM, so it's not sufficient for opening these files). I wouldn't think changing the operating system should make a difference, so that's why I was trying to confirm if there wasn't another setting I needed to change in Windows as opposed to Mac in order to change the memory settings. Thanks, Andrew P.S. Since we're at the same place, would it be easier to try to meet with you in person to talk about this issue? |
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Hi Andrew,
> The format is thousands of individual TIFF files compiled into a > folder. I collected the images using a Prairie scope (PrairieView > software), so I'm using the .XML file to open everything. OK, good to know. > I'm trying to open a fairly large file (3 GB) which is a Z series over > time with multiple stage locations totaling about 2800 images. We have lots of such data here at LOCI. We use the Fiji Stitching plugin to create mosaics. Do you need to do that, or is it sufficient for you to analyze each stage position individually? If you need a mosaic, have you tried following the instructions at: http://loci.wisc.edu/software/fiji-image-stitching ? Depending how you laid out your stage positions, you may also want to check the "Ignore Z stage position" option to control exactly how Z planes are stitched. (If this needs further explanation, I can improve the documentation to illustrate.) We also recently added a "Add tiles as ROIs" feature so that you can see where the original image plane positions fall within the mosaic (and track down which TIFF file each one came from). Lastly, if your mosaic is extremely large you can use the "Downsample tiles" feature to scale down each image plane as they are read in before they get stitched together. This can save a large amount of RAM. > I should also note that the file is on an external harddrive. At home > I was loading into a USB 3.0 port, but at work I only have USB 2.0 > ports. This shouldn't matter much (at most 2-3x difference) [1]. > I should note that I have never tried to open the files on a Windows > operating system Windows can have performance problems when there are many thousands of small files (as is the case for Prairie datasets). But the only way to know for certain would be to try it. I would suggest getting it working with the same configuration on a different OS first, though, if possible. > We have XP installed on our lab computers, but XP only recognizes > around 3GB of RAM, so it's not sufficient for opening these files. Yes, of course if you are running a 32-bit OS you will be limited in RAM. But e.g. Windows 7 64-bit should work. And even on 32-bit XP, with the "Use virtual stack" option checked, it should be possible to open and roam through your data since it is read on demand from disk in that mode. > that's why I was trying to confirm if there wasn't another setting I > needed to change in Windows as opposed to Mac in order to change the > memory settings. As far as ImageJ is concerned, there is no OS-specific memory setting anywhere. But again, as you point out, with 32-bit OSes you will be limited to ~1.5GB of RAM (as low as ~1.3GB on Windows XP), or ~3GB if you use the /3GB switch [2]. Regards, Curtis > P.S. Since we're at the same place, would it be easier to try to meet > with you in person to talk about this issue? Sure, if the Bio-Formats Importer's "Use virtual stack" option does not solve your problem, and/or you cannot get the Fiji Stitching plugin to work satisfactorily, we could meet to troubleshoot. Just keep me posted. [1] http://blogs.howstuffworks.com/2011/04/13/is-usb-3-0-really-faster-than-usb-2-0/ [2] http://msdn.microsoft.com/en-us/library/windows/hardware/ff556232(v=vs.85).aspx On Thu, Oct 3, 2013 at 12:09 PM, Andrew Riching <[hidden email]> wrote: > Hi Curtis, > > The format is thousands of individual TIFF files compiled into a folder. I > collected the images using a Prairie scope (PrairieView software), so I'm > using the .XML file to open everything. I have not tried a virtual stack, > but I can try that when I get home tonight. At work, I successfully opened > the file on a Mac 10.6.8 machine with 8 GB of RAM and a 2 GHz dual core > processor in 20 minutes. I should also note that the file is on an external > harddrive. At home I was loading into a USB 3.0 port, but at work I only > have USB 2.0 ports. In theory, every aspect of my home computer I would > expect to outperform the lab computer as far as hardware. I should note > that > I have never tried to open the files on a Windows operating system (We have > XP installed on our lab computers, but XP only recognizes around 3GB of > RAM, > so it's not sufficient for opening these files). I wouldn't think changing > the operating system should make a difference, so that's why I was trying > to > confirm if there wasn't another setting I needed to change in Windows as > opposed to Mac in order to change the memory settings. > > Thanks, > Andrew > > P.S. Since we're at the same place, would it be easier to try to meet with > you in person to talk about this issue? > > > > -- > View this message in context: > http://imagej.1557.x6.nabble.com/Memory-issue-tp5005018p5005028.html > Sent from the ImageJ mailing list archive at Nabble.com. > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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In reply to this post by Andrew Riching
Hi Andrew,
if you have the files on an external disk, what kind of filesystem is it? If it's a Mac File system (HFS+) that you read on a Windows machine using some third-party software, don't be astonished if it is slow. (Similarily, NTFS disks from Windows mounted on a Mac with FUSE are very slow). If it is a Windows filesystem (NTFS, FAT32, exFAT), I would be astonished to hear that it is faster on a Mac/USB 2.0 than on Windows/USB 3.0. Maybe you can determine the time to copy a few hundred files from the external HD to the internal one on both machines, to see whether reading the files from the HD is the problem? Then it would be unrelated to ImageJ. Michael ________________________________________________________________ On Oct 3, 2013, at 19:09, Andrew Riching wrote: > Hi Curtis, > > The format is thousands of individual TIFF files compiled into a folder. I > collected the images using a Prairie scope (PrairieView software), so I'm > using the .XML file to open everything. I have not tried a virtual stack, > but I can try that when I get home tonight. At work, I successfully opened > the file on a Mac 10.6.8 machine with 8 GB of RAM and a 2 GHz dual core > processor in 20 minutes. I should also note that the file is on an external > harddrive. At home I was loading into a USB 3.0 port, but at work I only > have USB 2.0 ports. In theory, every aspect of my home computer I would > expect to outperform the lab computer as far as hardware. I should note that > I have never tried to open the files on a Windows operating system (We have > XP installed on our lab computers, but XP only recognizes around 3GB of RAM, > so it's not sufficient for opening these files). I wouldn't think changing > the operating system should make a difference, so that's why I was trying to > confirm if there wasn't another setting I needed to change in Windows as > opposed to Mac in order to change the memory settings. > > Thanks, > Andrew > > P.S. Since we're at the same place, would it be easier to try to meet with > you in person to talk about this issue? -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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In reply to this post by ctrueden
Hi Curtis,
I don't need to stitch, I can analyze the stage positions separately. Once I get them all to open, I'll just use MTrackJ to track cells over time, so splitting them into separate hyperstacks for each stage position is all I want to do. The USB 3.0/2.0 thing was thrown in more for some of the posters above - I didn't think it would matter much, and my point was if anything, 3.0 should be faster (so my home set up should be better than at work). >Windows can have performance problems when there are many thousands of >small files (as is the case for Prairie datasets). But the only way to know >for certain would be to try it. I would suggest getting it working with the >same configuration on a different OS first, though, if possible. Do you mean get the files to open on a different OS first? If so, I am currently opening them on Mac OS10.6.8 just fine at work. The settings here are 5991 MB RAM with 2 threads. Or were you saying I should try another OS on my home computer if possible? I could also try using XP at work to load a virtual stack and see what happens. I'll update you when I've tried several of these things (so most likely later tonight, after I've had a chance to mess around with some of the suggestions you've given me at home). For Michael: My external has 2 partitions - one is mac-specific and is used for backups. The other partition is FAT32 so I can use it for both Mac and Windows storage. This is the partition I'm trying to open files from. I really don't think the issue has to do with my hard drive or my computer's hardware, but could be related to what OS I'm using, as Curtis mentioned Windows can have performance problems when opening many individual files. |
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Alright, I've tested out a few things now. While I was at work, I tried opening files as virtual stacks on Windows XP, Windows 7, and MacOS 10.8.3. XP and 7 were significantly slower (it probably took between 3 to 5 minutes to open the file on either OS). MacOS 10.8.3 took maybe 30 seconds to open the file as a virtual stack.
When I got home, I set my memory and threads settings to 5991 MB RAM, 2 threads (as this was the set up I had at work) and tried opening as a virtual stack. On my home computer, I got the file to open in about a minute, maybe a little longer. I tried changing the memory and threads to 12000 MB RAM, 8 threads, but I don't think this made a big difference on how long it took to open the file. -Andrew |
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Hi Andrew,
On Thu, 3 Oct 2013, Andrew Riching wrote: > Alright, I've tested out a few things now. While I was at work, I tried > opening files as virtual stacks on Windows XP, Windows 7, and MacOS > 10.8.3. XP and 7 were significantly slower (it probably took between 3 > to 5 minutes to open the file on either OS). MacOS 10.8.3 took maybe 30 > seconds to open the file as a virtual stack. That sounds consistent with a virus scanner (required on Windows, but maybe not so much for .tif files). Ciao, Johannes -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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In reply to this post by Hongbo Zhang
Hi Hongbo,
I didn't see an answer to your question though I may have missed it. Do you mean something like Edit - Selection - Specify (pixels)? You can also store the ROIs in the ROI Manager to reuse. Kind regards, Jacqui Jacqueline Ross Biomedical Imaging Microscopist Biomedical Imaging Research Unit School of Medical Sciences Faculty of Medical & Health Sciences The University of Auckland Private Bag 92019 Auckland 1142, NEW ZEALAND Tel: 64 9 923 7438 Fax: 64 9 373 7484 http://www.fmhs.auckland.ac.nz/sms/biru/ -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Hongbo Zhang Sent: Thursday, 3 October 2013 7:48 p.m. To: [hidden email] Subject: Rectanglar tool using Hey all, A short question: Does anybody know how to set up the size of "Rectanglar tool"? For instance, draw a rectangular with 500x800um in a normalized picture or even pixels in the original picture (e.g. make the square with a set size but not adjust it carefully)? Thank you very much in advance! Cheers, Hongbo On Oct 3, 2013, at 5:22 AM, Aaron Hendrickson <[hidden email]> wrote: > Andrew, > I am not sure why it's loading so slow for you. Have you tried > opening the images as a virtual stack? That may not be what you want > but it will certainly load faster (at the cost of slower processing). > Also, you might want to close ImageJ and try opening the stack again. > I hope this helps a little. > > -Aaron > > > On Wed, Oct 2, 2013 at 10:21 PM, Andrew Riching <[hidden email]> wrote: > >> Apologies if this has been addressed before - I searched for my issue >> in previous threads, but hadn't seen the specific problem I'm having anywhere. >> I'm trying to open a fairly large file (3 GB) which is a Z series >> over time with multiple stage locations totaling about 2800 images. >> I've opened these routinely on a mac mini running both 10.6.8 and >> 10.7, with the computer having 8 GB of RAM. Generally, they open in about 10 minutes. >> >> Right now I'm working at home on a 64 bit Windows 7 machine with an >> intel >> i7 >> 3.4 GHz processor with 16 GB of RAM on a 64 bit version of FIJI, so I >> would expect the files to open even faster, however this isn't >> happening. I haven't gotten one to open at all yet, and I've been waiting over an hour. >> I >> checked the memory and threads, and it's set to use 12000 MB of >> memory (so the 75% of the total memory that was recommended on the >> FIJI wiki) with 8 threads and the "Run garbage collector on status >> bar" box is checked. I have tried using less threads and less memory, >> but the results don't change. I am monitoring the computer's >> performance, and the CPU usage shifts between 12% and 15% while the >> memory usage is between 4.00 and 4.7 GB, generally with at least 8GB >> "free." >> >> Is there something I'm overlooking about changing the memory allocation? >> FIJI seems to ignore whatever I set. >> >> Thanks, >> -Andrew >> >> >> >> -- >> View this message in context: >> http://imagej.1557.x6.nabble.com/Memory-issue-tp5005018.html >> Sent from the ImageJ mailing list archive at Nabble.com. >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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