jpg2000 and mxrs in imagej
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Hi,
I'm struggling with export of very large .mrxs (mirax) files. These are scans from a slide scanner that I intend to analyze further in ImageJ. I found a tool called JP2 WSI converter. It seems really good, because it can batch-convert huge mrxs files into jpg2000. The problem is that even if ImageJ2 data structures and SCIFIO are enabled, the program cannot load the files. Before I enabled them I was getting a following message: java.lang.IllegalArgumentException: Array size too large: 33280 x 105216 x 1 After enabling ImageJ2 data structures and SCIFIO the memory gets flooded and the software gets stuck (work on a workstation with 6 cores, 6 threads and 64 GB of memory). Thanks for help! Filip -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Filip,
I've no experience with ImageJ2 data structures and don't know about their limits, but what does "x 1" mean in "33280 x 105216 x 1"? Does it indicate a single image, i.e. no stack, or does it stand for a binary-valued image? If it is not a binary-valued image, what is its bit-depth? Best Herbie ::::::::::::::::::::::::::::::::::::::::::: Am 06.12.15 um 14:56 schrieb Filip Bochner: > Hi, > > I'm struggling with export of very large .mrxs (mirax) files. These > are scans from a slide scanner that I intend to analyze further in > ImageJ. > > I found a tool called JP2 WSI converter. It seems really good, > because it can batch-convert huge mrxs files into jpg2000. > > The problem is that even if ImageJ2 data structures and SCIFIO are > enabled, the program cannot load the files. > > Before I enabled them I was getting a following message: > java.lang.IllegalArgumentException: Array size too large: 33280 x > 105216 x 1 > > After enabling ImageJ2 data structures and SCIFIO the memory gets > flooded and the software gets stuck (work on a workstation with 6 > cores, 6 threads and 64 GB of memory). > > Thanks for help! > > Filip > > > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Filip,
evidently, RGB 0 bit doesn't make sense -- no? Usually, RGB means 24bit per pixel which results in about 10.5 GByte for your image. I don't know why ImageJ2 can't deal with 10.5 GByte images, but I know that the old data structures of Java, hence ImageJ, are can't. "[...] the program cannot load the files" I guess with "program" you mean "Fiji". BTW, which _slide_ scanner provides "33280 x 105216" pixels per image? What kind of slides (format?) do have such spatial resolution? Best Herbie ::::::::::::::::::::::::::::::::::::::::::: Am 06.12.15 um 16:04 schrieb Filip Bochner: > Hi Herbie, > > "x 1" means that this is just one image. If it was a stack with let's > say 13 images it would say "x 13". > > NIS-elements viewer (which just opens the images) shows RGB 0 bit. > > Filip > > -----Original Message----- From: ImageJ Interest Group > [mailto:[hidden email]] On Behalf Of Herbie Sent: Sunday, > December 06, 2015 4:46 PM To: [hidden email] Subject: Re: > jpg2000 and mxrs in imagej > > Filip, > > I've no experience with ImageJ2 data structures and don't know about > their limits, but what does "x 1" mean in "33280 x 105216 x 1"? Does > it indicate a single image, i.e. no stack, or does it stand for a > binary-valued image? > > If it is not a binary-valued image, what is its bit-depth? > > Best > > Herbie > > ::::::::::::::::::::::::::::::::::::::::::: Am 06.12.15 um 14:56 > schrieb Filip Bochner: >> Hi, >> >> I'm struggling with export of very large .mrxs (mirax) files. >> These are scans from a slide scanner that I intend to analyze >> further in ImageJ. >> >> I found a tool called JP2 WSI converter. It seems really good, >> because it can batch-convert huge mrxs files into jpg2000. >> >> The problem is that even if ImageJ2 data structures and SCIFIO are >> enabled, the program cannot load the files. >> >> Before I enabled them I was getting a following message: >> java.lang.IllegalArgumentException: Array size too large: 33280 x >> 105216 x 1 >> >> After enabling ImageJ2 data structures and SCIFIO the memory gets >> flooded and the software gets stuck (work on a workstation with 6 >> cores, 6 threads and 64 GB of memory). >> >> Thanks for help! >> >> Filip -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Filip,
I found your explanations quite helpful and I hope that those on the list who may help further, also get a better impression of the kind of images you are dealing with. If you can separately access the 4096x4096 images, my recommendation is to do the tiling in Fiji which more or less implies to rely on TIF as the file format. HTH Herbie ::::::::::::::::::::::::::::::::::::::::::: Am 06.12.15 um 18:22 schrieb Filip Bochner: > Herbie, > > Of course you're right. I couldn't see what is the bit depth in > properties of the file. I would also guess it's 24bit. Apparently > Image Viewer displayed it incorrectly. And I trusted it > unfortunately. > > Yes, we keep talking about Fiji :) > > The slide scanner' name's Panoramic Midi. It saves the files in .mrxs > format. Each .mrxs is accompanied with a folder of .dat files. In > principle it's a tiled image that can be viewed by free Panoramic > Viewer (that doesn't have a batch export and it's poorly written so > the conversion of single ROI takes forever and I have tens of slides > with tens of ROIs and will have even more). A single scan gives > 4096x4096 resolution images, but there is an array of them, which > after export gives a huge matrix. > > I don't think it's a size (gb) problem, since I opened much larger > files in Fiji. It could be an array-size problem. It might not be > even related to the format, but I'm not sure whether .tiff of similar > size would give the same error (or crash). > > Filip > > Wysłane z iPada > > Dnia 06.12.2015 o godz. 17:26 Herbie <[hidden email]> napisał(a): > >> Filip, >> >> evidently, RGB 0 bit doesn't make sense -- no? >> >> Usually, RGB means 24bit per pixel which results in about 10.5 >> GByte for your image. I don't know why ImageJ2 can't deal with 10.5 >> GByte images, but I know that the old data structures of Java, >> hence ImageJ, are can't. >> >> "[...] the program cannot load the files" I guess with "program" >> you mean "Fiji". >> >> BTW, which _slide_ scanner provides "33280 x 105216" pixels per >> image? What kind of slides (format?) do have such spatial >> resolution? >> >> Best >> >> Herbie >> >> ::::::::::::::::::::::::::::::::::::::::::: >>> Am 06.12.15 um 16:04 schrieb Filip Bochner: Hi Herbie, >>> >>> "x 1" means that this is just one image. If it was a stack with >>> let's say 13 images it would say "x 13". >>> >>> NIS-elements viewer (which just opens the images) shows RGB 0 >>> bit. >>> >>> Filip >>> >>> -----Original Message----- From: ImageJ Interest Group >>> [mailto:[hidden email]] On Behalf Of Herbie Sent: Sunday, >>> December 06, 2015 4:46 PM To: [hidden email] Subject: Re: >>> jpg2000 and mxrs in imagej >>> >>> Filip, >>> >>> I've no experience with ImageJ2 data structures and don't know >>> about their limits, but what does "x 1" mean in "33280 x 105216 x >>> 1"? Does it indicate a single image, i.e. no stack, or does it >>> stand for a binary-valued image? >>> >>> If it is not a binary-valued image, what is its bit-depth? >>> >>> Best >>> >>> Herbie >>> >>> ::::::::::::::::::::::::::::::::::::::::::: Am 06.12.15 um 14:56 >>> schrieb Filip Bochner: >>>> Hi, >>>> >>>> I'm struggling with export of very large .mrxs (mirax) files. >>>> These are scans from a slide scanner that I intend to analyze >>>> further in ImageJ. >>>> >>>> I found a tool called JP2 WSI converter. It seems really good, >>>> because it can batch-convert huge mrxs files into jpg2000. >>>> >>>> The problem is that even if ImageJ2 data structures and SCIFIO >>>> are enabled, the program cannot load the files. >>>> >>>> Before I enabled them I was getting a following message: >>>> java.lang.IllegalArgumentException: Array size too large: 33280 >>>> x 105216 x 1 >>>> >>>> After enabling ImageJ2 data structures and SCIFIO the memory >>>> gets flooded and the software gets stuck (work on a workstation >>>> with 6 cores, 6 threads and 64 GB of memory). >>>> >>>> Thanks for help! >>>> >>>> Filip > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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In reply to this post by Filip Bochner
Hi Filip,
> After enabling ImageJ2 data structures and SCIFIO It sounds like you are running an old version of Fiji. For various reasons, I suggest you upgrade to the latest version. However, in this case doing so will not solve the issue at hand. > IllegalArgumentException: Array size too large: 33280 x 105216 x 1 ImageJ only supports planes up to 2Gpix. See also http://imagej.net/Troubleshooting#NegativeArraySizeException. As a workaround, I second Herbie's suggestion to work with your image in tiles. You can use the "Crop on import" option on the Bio-Formats Import Options dialog. Regards, Curtis On Sun, Dec 6, 2015 at 7:56 AM, Filip Bochner <[hidden email]> wrote: > Hi, > > I'm struggling with export of very large .mrxs (mirax) files. These are > scans from a slide scanner that I intend to analyze further in ImageJ. > > I found a tool called JP2 WSI converter. It seems really good, because it > can batch-convert huge mrxs files into jpg2000. > > The problem is that even if ImageJ2 data structures and SCIFIO are > enabled, the program cannot load the files. > > Before I enabled them I was getting a following message: > java.lang.IllegalArgumentException: Array size too large: 33280 x 105216 x 1 > > After enabling ImageJ2 data structures and SCIFIO the memory gets flooded > and the software gets stuck (work on a workstation with 6 cores, 6 threads > and 64 GB of memory). > > Thanks for help! > > Filip > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Good day Curtis,
I'm a bit surprised that ImageJ-2/SCIFIO is limited to the same amount of pixels (array size) as ImageJ-1. I thought that it uses the newer Java BIG number formats that should allow for much larger arrays. Do I confuse or did I miss something? In my response to Filip I thought that the problem only concerns the io-section of ImageJ-2, i.e. "Bio-Formats" or the like. Eager to learn more about this aspect of ImageJ-2 Herbie ::::::::::::::::::::::::::::::::::::::::::: Am 07.12.15 um 04:54 schrieb Curtis Rueden: > Hi Filip, > >> After enabling ImageJ2 data structures and SCIFIO > > It sounds like you are running an old version of Fiji. For various reasons, > I suggest you upgrade to the latest version. However, in this case doing so > will not solve the issue at hand. > >> IllegalArgumentException: Array size too large: 33280 x 105216 x 1 > > ImageJ only supports planes up to 2Gpix. See also > http://imagej.net/Troubleshooting#NegativeArraySizeException. > > As a workaround, I second Herbie's suggestion to work with your image in > tiles. You can use the "Crop on import" option on the Bio-Formats Import > Options dialog. > > Regards, > Curtis > > > On Sun, Dec 6, 2015 at 7:56 AM, Filip Bochner <[hidden email]> > wrote: > >> Hi, >> >> I'm struggling with export of very large .mrxs (mirax) files. These are >> scans from a slide scanner that I intend to analyze further in ImageJ. >> >> I found a tool called JP2 WSI converter. It seems really good, because it >> can batch-convert huge mrxs files into jpg2000. >> >> The problem is that even if ImageJ2 data structures and SCIFIO are >> enabled, the program cannot load the files. >> >> Before I enabled them I was getting a following message: >> java.lang.IllegalArgumentException: Array size too large: 33280 x 105216 x 1 >> >> After enabling ImageJ2 data structures and SCIFIO the memory gets flooded >> and the software gets stuck (work on a workstation with 6 cores, 6 threads >> and 64 GB of memory). >> >> Thanks for help! >> >> Filip >> >> >> -- >> 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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In reply to this post by Herbie
Filip,
if, as Curtis tells us, ImageJ-2/SCIFIO shows the same limited array size as ImageJ-1, that actually is a limitation due to "classic" Java, then I see no chance for handling images as large as yours. Best Herbie ::::::::::::::::::::::::::::::::::::::::::: Am 06.12.15 um 20:06 schrieb Filip Bochner: > Herbie, thanks for your input. There is no way to get into the single > tiles. Probably some programing must be involved there, and that for > now exceeds my capabilities. I'm a biologist trying to get the stuff > done in the simplest way possible. I hope there is a simple way, and > the imagej problem can be solved. > > Any other ideas? > > > > Wysłane z iPada > > Dnia 06.12.2015 o godz. 19:37 Herbie <[hidden email]> napisał(a): > >> Filip, >> >> I found your explanations quite helpful and I hope that those on >> the list who may help further, also get a better impression of the >> kind of images you are dealing with. >> >> If you can separately access the 4096x4096 images, my >> recommendation is to do the tiling in Fiji which more or less >> implies to rely on TIF as the file format. >> >> HTH >> >> Herbie >> >> ::::::::::::::::::::::::::::::::::::::::::: >>> Am 06.12.15 um 18:22 schrieb Filip Bochner: Herbie, >>> >>> Of course you're right. I couldn't see what is the bit depth in >>> properties of the file. I would also guess it's 24bit. >>> Apparently Image Viewer displayed it incorrectly. And I trusted >>> it unfortunately. >>> >>> Yes, we keep talking about Fiji :) >>> >>> The slide scanner' name's Panoramic Midi. It saves the files in >>> .mrxs format. Each .mrxs is accompanied with a folder of .dat >>> files. In principle it's a tiled image that can be viewed by free >>> Panoramic Viewer (that doesn't have a batch export and it's >>> poorly written so the conversion of single ROI takes forever and >>> I have tens of slides with tens of ROIs and will have even more). >>> A single scan gives 4096x4096 resolution images, but there is an >>> array of them, which after export gives a huge matrix. >>> >>> I don't think it's a size (gb) problem, since I opened much >>> larger files in Fiji. It could be an array-size problem. It might >>> not be even related to the format, but I'm not sure whether .tiff >>> of similar size would give the same error (or crash). >>> >>> Filip >>> >>> Wysłane z iPada >>> >>> Dnia 06.12.2015 o godz. 17:26 Herbie <[hidden email]> >>> napisał(a): >>> >>>> Filip, >>>> >>>> evidently, RGB 0 bit doesn't make sense -- no? >>>> >>>> Usually, RGB means 24bit per pixel which results in about 10.5 >>>> GByte for your image. I don't know why ImageJ2 can't deal with >>>> 10.5 GByte images, but I know that the old data structures of >>>> Java, hence ImageJ, are can't. >>>> >>>> "[...] the program cannot load the files" I guess with >>>> "program" you mean "Fiji". >>>> >>>> BTW, which _slide_ scanner provides "33280 x 105216" pixels >>>> per image? What kind of slides (format?) do have such spatial >>>> resolution? >>>> >>>> Best >>>> >>>> Herbie >>>> >>>> ::::::::::::::::::::::::::::::::::::::::::: >>>>> Am 06.12.15 um 16:04 schrieb Filip Bochner: Hi Herbie, >>>>> >>>>> "x 1" means that this is just one image. If it was a stack >>>>> with let's say 13 images it would say "x 13". >>>>> >>>>> NIS-elements viewer (which just opens the images) shows RGB >>>>> 0 bit. >>>>> >>>>> Filip >>>>> >>>>> -----Original Message----- From: ImageJ Interest Group >>>>> [mailto:[hidden email]] On Behalf Of Herbie Sent: >>>>> Sunday, December 06, 2015 4:46 PM To: [hidden email] >>>>> Subject: Re: jpg2000 and mxrs in imagej >>>>> >>>>> Filip, >>>>> >>>>> I've no experience with ImageJ2 data structures and don't >>>>> know about their limits, but what does "x 1" mean in "33280 x >>>>> 105216 x 1"? Does it indicate a single image, i.e. no stack, >>>>> or does it stand for a binary-valued image? >>>>> >>>>> If it is not a binary-valued image, what is its bit-depth? >>>>> >>>>> Best >>>>> >>>>> Herbie >>>>> >>>>> ::::::::::::::::::::::::::::::::::::::::::: Am 06.12.15 um >>>>> 14:56 schrieb Filip Bochner: >>>>>> Hi, >>>>>> >>>>>> I'm struggling with export of very large .mrxs (mirax) >>>>>> files. These are scans from a slide scanner that I intend >>>>>> to analyze further in ImageJ. >>>>>> >>>>>> I found a tool called JP2 WSI converter. It seems really >>>>>> good, because it can batch-convert huge mrxs files into >>>>>> jpg2000. >>>>>> >>>>>> The problem is that even if ImageJ2 data structures and >>>>>> SCIFIO are enabled, the program cannot load the files. >>>>>> >>>>>> Before I enabled them I was getting a following message: >>>>>> java.lang.IllegalArgumentException: Array size too large: >>>>>> 33280 x 105216 x 1 >>>>>> >>>>>> After enabling ImageJ2 data structures and SCIFIO the >>>>>> memory gets flooded and the software gets stuck (work on a >>>>>> workstation with 6 cores, 6 threads and 64 GB of memory). >>>>>> >>>>>> Thanks for help! >>>>>> >>>>>> Filip >> >> -- 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 ctrueden
Hi Curtis and Herbie,
> It sounds like you are running an old version of Fiji. For various reasons, I suggest you upgrade to the latest version. However, in this case doing so will not solve the issue at hand. This is what I just did. I downloaded FIJI again and updated it through the update tool. Still I get the same error about the array size. > ImageJ only supports planes up to 2Gpix. See also http://imagej.net/Troubleshooting#NegativeArraySizeException. As a workaround, I second Herbie's suggestion to work with your image in tiles. You can use the "Crop on import" option on the Bio-Formats Import Options dialog Unfortunately "Crop on import still doesn't work. As I understand X Coordinate 1 and Y Coordinate 1 are the coordinates that specify where to start cropping the matrix. Width 1 and Height 1 are probably the sizes of the single tile? It still doesn't work with such input I get the same error about the array size. I suspect that FIJI has to load it first in order to crop it, so it leads to the same problem. What do you think? > if, as Curtis tells us, ImageJ-2/SCIFIO shows the same limited array size as ImageJ-1, that actually is a limitation due to "classic" Java, then I see no chance for handling images as large as yours Is this problem going to be addressed in the future? I understand for now there is no way to do it? If not the only option is to use the python library called "openslide" and then maybe MATLAB? Would MATLAB handle such a big maps? Thanks Filip -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Curtis Rueden Sent: Monday, December 07, 2015 5:55 AM To: [hidden email] Subject: Re: jpg2000 and mxrs in imagej Hi Filip, > After enabling ImageJ2 data structures and SCIFIO It sounds like you are running an old version of Fiji. For various reasons, I suggest you upgrade to the latest version. However, in this case doing so will not solve the issue at hand. > IllegalArgumentException: Array size too large: 33280 x 105216 x 1 ImageJ only supports planes up to 2Gpix. See also http://imagej.net/Troubleshooting#NegativeArraySizeException. As a workaround, I second Herbie's suggestion to work with your image in tiles. You can use the "Crop on import" option on the Bio-Formats Import Options dialog. Regards, Curtis On Sun, Dec 6, 2015 at 7:56 AM, Filip Bochner <[hidden email]> wrote: > Hi, > > I'm struggling with export of very large .mrxs (mirax) files. These > are scans from a slide scanner that I intend to analyze further in ImageJ. > > I found a tool called JP2 WSI converter. It seems really good, because > it can batch-convert huge mrxs files into jpg2000. > > The problem is that even if ImageJ2 data structures and SCIFIO are > enabled, the program cannot load the files. > > Before I enabled them I was getting a following message: > java.lang.IllegalArgumentException: Array size too large: 33280 x > 105216 x 1 > > After enabling ImageJ2 data structures and SCIFIO the memory gets > flooded and the software gets stuck (work on a workstation with 6 > cores, 6 threads and 64 GB of memory). > > Thanks for help! > > Filip > > > -- > 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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Dear Curtis, Herbie and Filip,
Did not follow this discussion closely but I thought that TrackEM2 plugin is able to open large datasets? Found on their website "•Very large images (like 21k x 21k) are now handled much better; only waiting time is for loading the file." Best wishes Kees Dr Ir K.R. Straatman Senior Experimental Officer Advanced Imaging Facility Centre for Core Biotechnology Services University of Leicester http://www2.le.ac.uk/colleges/medbiopsych/facilities-and-services/cbs/lite/aif -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Filip Bochner Sent: 07 December 2015 10:06 To: [hidden email] Subject: Re: jpg2000 and mxrs in imagej Hi Curtis and Herbie, > It sounds like you are running an old version of Fiji. For various reasons, I suggest you upgrade to the latest version. However, in this case doing so will not solve the issue at hand. This is what I just did. I downloaded FIJI again and updated it through the update tool. Still I get the same error about the array size. > ImageJ only supports planes up to 2Gpix. See also > http://imagej.net/Troubleshooting#NegativeArraySizeException. As a > workaround, I second Herbie's suggestion to work with your image in > tiles. You can use the "Crop on import" option on the Bio-Formats > Import Options dialog Unfortunately "Crop on import still doesn't work. As I understand X Coordinate 1 and Y Coordinate 1 are the coordinates that specify where to start cropping the matrix. Width 1 and Height 1 are probably the sizes of the single tile? It still doesn't work with such input I get the same error about the array size. I suspect that FIJI has to load it first in order to crop it, so it leads to the same problem. What do you think? > if, as Curtis tells us, ImageJ-2/SCIFIO shows the same limited array > size as ImageJ-1, that actually is a limitation due to "classic" Java, > then I see no chance for handling images as large as yours Is this problem going to be addressed in the future? I understand for now there is no way to do it? If not the only option is to use the python library called "openslide" and then maybe MATLAB? Would MATLAB handle such a big maps? Thanks Filip -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Curtis Rueden Sent: Monday, December 07, 2015 5:55 AM To: [hidden email] Subject: Re: jpg2000 and mxrs in imagej Hi Filip, > After enabling ImageJ2 data structures and SCIFIO It sounds like you are running an old version of Fiji. For various reasons, I suggest you upgrade to the latest version. However, in this case doing so will not solve the issue at hand. > IllegalArgumentException: Array size too large: 33280 x 105216 x 1 ImageJ only supports planes up to 2Gpix. See also http://imagej.net/Troubleshooting#NegativeArraySizeException. As a workaround, I second Herbie's suggestion to work with your image in tiles. You can use the "Crop on import" option on the Bio-Formats Import Options dialog. Regards, Curtis On Sun, Dec 6, 2015 at 7:56 AM, Filip Bochner <[hidden email]> wrote: > Hi, > > I'm struggling with export of very large .mrxs (mirax) files. These > are scans from a slide scanner that I intend to analyze further in ImageJ. > > I found a tool called JP2 WSI converter. It seems really good, because > it can batch-convert huge mrxs files into jpg2000. > > The problem is that even if ImageJ2 data structures and SCIFIO are > enabled, the program cannot load the files. > > Before I enabled them I was getting a following message: > java.lang.IllegalArgumentException: Array size too large: 33280 x > 105216 x 1 > > After enabling ImageJ2 data structures and SCIFIO the memory gets > flooded and the software gets stuck (work on a workstation with 6 > cores, 6 threads and 64 GB of memory). > > Thanks for help! > > Filip > > > -- > 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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Dear Kees,
thanks for chiming in but Filip has to deal with much larger images of about 33k x 105k pixels. I'm sure that this is beyond classic Java's array size. Have a good day Herbie ::::::::::::::::::::::::::::::::::::::::::::::::::: Am 07.12.15 um 18:03 schrieb Straatman, Kees (Dr.): > Dear Curtis, Herbie and Filip, > > Did not follow this discussion closely but I thought that TrackEM2 > plugin is able to open large datasets? Found on their website "•Very > large images (like 21k x 21k) are now handled much better; only > waiting time is for loading the file." > > Best wishes > > Kees > > > Dr Ir K.R. Straatman Senior Experimental Officer Advanced Imaging > Facility Centre for Core Biotechnology Services University of > Leicester > http://www2.le.ac.uk/colleges/medbiopsych/facilities-and-services/cbs/lite/aif > > > > -----Original Message----- From: ImageJ Interest Group > [mailto:[hidden email]] On Behalf Of Filip Bochner Sent: 07 > December 2015 10:06 To: [hidden email] Subject: Re: jpg2000 and > mxrs in imagej > > Hi Curtis and Herbie, > >> It sounds like you are running an old version of Fiji. For various >> reasons, I suggest you upgrade to the latest version. However, in >> this case doing so will not solve the issue at hand. > > This is what I just did. I downloaded FIJI again and updated it > through the update tool. Still I get the same error about the array > size. > >> ImageJ only supports planes up to 2Gpix. See also >> http://imagej.net/Troubleshooting#NegativeArraySizeException. As a >> workaround, I second Herbie's suggestion to work with your image >> in tiles. You can use the "Crop on import" option on the >> Bio-Formats Import Options dialog > > Unfortunately "Crop on import still doesn't work. As I understand X > Coordinate 1 and Y Coordinate 1 are the coordinates that specify > where to start cropping the matrix. Width 1 and Height 1 are probably > the sizes of the single tile? It still doesn't work with such input I > get the same error about the array size. I suspect that FIJI has to > load it first in order to crop it, so it leads to the same problem. > What do you think? > >> if, as Curtis tells us, ImageJ-2/SCIFIO shows the same limited >> array size as ImageJ-1, that actually is a limitation due to >> "classic" Java, then I see no chance for handling images as large >> as yours > > Is this problem going to be addressed in the future? I understand for > now there is no way to do it? If not the only option is to use the > python library called "openslide" and then maybe MATLAB? Would MATLAB > handle such a big maps? > > Thanks > > Filip > > > -----Original Message----- From: ImageJ Interest Group > [mailto:[hidden email]] On Behalf Of Curtis Rueden Sent: Monday, > December 07, 2015 5:55 AM To: [hidden email] Subject: Re: > jpg2000 and mxrs in imagej > > Hi Filip, > >> After enabling ImageJ2 data structures and SCIFIO > > It sounds like you are running an old version of Fiji. For various > reasons, I suggest you upgrade to the latest version. However, in > this case doing so will not solve the issue at hand. > >> IllegalArgumentException: Array size too large: 33280 x 105216 x 1 > > ImageJ only supports planes up to 2Gpix. See also > http://imagej.net/Troubleshooting#NegativeArraySizeException. > > As a workaround, I second Herbie's suggestion to work with your image > in tiles. You can use the "Crop on import" option on the Bio-Formats > Import Options dialog. > > Regards, Curtis > > > On Sun, Dec 6, 2015 at 7:56 AM, Filip Bochner > <[hidden email]> wrote: > >> Hi, >> >> I'm struggling with export of very large .mrxs (mirax) files. >> These are scans from a slide scanner that I intend to analyze >> further in ImageJ. >> >> I found a tool called JP2 WSI converter. It seems really good, >> because it can batch-convert huge mrxs files into jpg2000. >> >> The problem is that even if ImageJ2 data structures and SCIFIO are >> enabled, the program cannot load the files. >> >> Before I enabled them I was getting a following message: >> java.lang.IllegalArgumentException: Array size too large: 33280 x >> 105216 x 1 >> >> After enabling ImageJ2 data structures and SCIFIO the memory gets >> flooded and the software gets stuck (work on a workstation with 6 >> cores, 6 threads and 64 GB of memory). >> >> Thanks for help! >> >> Filip >> >> >> -- 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 > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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In reply to this post by Herbie
Hi Herbie,
> I'm a bit surprised that ImageJ-2/SCIFIO is limited to the same amount > of pixels (array size) as ImageJ-1. I thought that it uses the newer > Java BIG number formats that should allow for much larger arrays. Do I > confuse or did I miss something? The limitation is on the ImageJ 1.x side. ImageJ2 and Fiji still use ImageJ 1.x as the default user interface. Image data structures must be translated between IJ1 and IJ2, so the 2 Gpix bottleneck still applies. The ImgLib2 library and ImageJ common data model support N-dimensional images in an extensible interface-driven way, with N<=2^31-1 and of length 2^63-1 each. Regards, Curtis On Mon, Dec 7, 2015 at 3:26 AM, Herbie <[hidden email]> wrote: > Good day Curtis, > > I'm a bit surprised that ImageJ-2/SCIFIO is limited to the same amount of > pixels (array size) as ImageJ-1. I thought that it uses the newer Java BIG > number formats that should allow for much larger arrays. Do I confuse or > did I miss something? > > In my response to Filip I thought that the problem only concerns the > io-section of ImageJ-2, i.e. "Bio-Formats" or the like. > > Eager to learn more about this aspect of ImageJ-2 > > Herbie > > ::::::::::::::::::::::::::::::::::::::::::: > Am 07.12.15 um 04:54 schrieb Curtis Rueden: > > Hi Filip, >> >> After enabling ImageJ2 data structures and SCIFIO >>> >> >> It sounds like you are running an old version of Fiji. For various >> reasons, >> I suggest you upgrade to the latest version. However, in this case doing >> so >> will not solve the issue at hand. >> >> IllegalArgumentException: Array size too large: 33280 x 105216 x 1 >>> >> >> ImageJ only supports planes up to 2Gpix. See also >> http://imagej.net/Troubleshooting#NegativeArraySizeException. >> >> As a workaround, I second Herbie's suggestion to work with your image in >> tiles. You can use the "Crop on import" option on the Bio-Formats Import >> Options dialog. >> >> Regards, >> Curtis >> >> >> On Sun, Dec 6, 2015 at 7:56 AM, Filip Bochner < >> [hidden email]> >> wrote: >> >> Hi, >>> >>> I'm struggling with export of very large .mrxs (mirax) files. These are >>> scans from a slide scanner that I intend to analyze further in ImageJ. >>> >>> I found a tool called JP2 WSI converter. It seems really good, because it >>> can batch-convert huge mrxs files into jpg2000. >>> >>> The problem is that even if ImageJ2 data structures and SCIFIO are >>> enabled, the program cannot load the files. >>> >>> Before I enabled them I was getting a following message: >>> java.lang.IllegalArgumentException: Array size too large: 33280 x 105216 >>> x 1 >>> >>> After enabling ImageJ2 data structures and SCIFIO the memory gets flooded >>> and the software gets stuck (work on a workstation with 6 cores, 6 >>> threads >>> and 64 GB of memory). >>> >>> Thanks for help! >>> >>> Filip >>> >>> >>> -- >>> 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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