ImageJ driving AVT Guppy CCD cam
Locked
 
|
Could someone help me answering some metaphysical question related to ImageJ?
I would like to interface my AVT Guppy CCD camera (see eg http://www.firstsightvision.co.uk/cameras/avt-guppy.html) with ImageJ for grabbing images or image sequences. Does someone know whether it is possible, and if yes how to do? Are the Scion or the twain or any other packages helpful for that? Many thanks... |
|
|
Luc,
You could try the CivilCapture plugin. If your camera has a working driver on your system, it is likely that LTI-Civil can use it. See http://lti-civil.org/ for the library, and http://www.eslide.net/civilcapture.php for the ImageJ plugin using it. Jerome. On Jan 2, 2008 7:17 PM, luc****** <[hidden email]> wrote: > Could someone help me answering some metaphysical question related to > ImageJ? > I would like to interface my AVT Guppy CCD camera (see eg > http://www.firstsightvision.co.uk/cameras/avt-guppy.html) with ImageJ for > grabbing images or image sequences. Does someone know whether it is > possible, and if yes how to do? Are the Scion or the twain or any other > packages helpful for that? > Many thanks... > -- > View this message in context: > http://www.nabble.com/ImageJ-driving-AVT-Guppy-CCD-cam-tp14401278p14401278.html > Sent from the ImageJ mailing list archive at Nabble.com. > |
|
|
Dear ImageJ:
I have a naive question for imageJ group. In our lab, we have Aperio scanscope. The image file is svs file. The image analysis tools of Aperio are limited. I would like do image analysis of these svs file by using imageJ. Can anyone tell me if I am able to open svs file in imageJ Best Regards, Yan ===================================== Yan Gao, Doctoral of Science, HTL (ASCP) Novartis Institutes for BioMedical Research _________________________ CONFIDENTIALITY NOTICE The information contained in this e-mail message is intended only for the exclusive use of the individual or entity named above and may contain information that is privileged, confidential or exempt from disclosure under applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivery of the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately by e-mail and delete the material from any computer. Thank you. |
Re: I would like doing image analysis of svs file by using imageJ
|
|
We also have an Aperio Scanscope and would like to do something similar
within imageJ. We use Image Pro Plus and the Aperio IPPMacro plugin on occasion. This works well for some applications. We are just in the beginning stages of working with this. This method can make use of layers drawn within ImageScope. You can have IPP process these layers. You can extract regions of interest inside of the ImageScope application (to jpg or tiff) and then analyze using ImageJ, but there is no way to directly use imageJ on an svs file that I am aware of. Aperio has a SDK that you can use with MS visual studio (C++) to build custom algorithms to run inside of ImageScope. I have no experience with this yet. Perhaps with the SDK you could build something that could use ImageJ... Also you can use Matlab to analyze images. I have some simple example .m files from Aperio that show how to read in sequential image pieces from an svs file and process them. Unfortunately, this procedure cannot utilize the markup layers. It is basically a sliding window that moves across the image. What is your specific application? Ryan Deaton Pathology Information Systems Specialist University of Illinois at Chicago 312-355-4338 -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Yan Gao Sent: Friday, January 04, 2008 1:56 PM To: [hidden email] Subject: I would like doing image analysis of svs file by using imageJ Dear ImageJ: I have a naive question for imageJ group. In our lab, we have Aperio scanscope. The image file is svs file. The image analysis tools of Aperio are limited. I would like do image analysis of these svs file by using imageJ. Can anyone tell me if I am able to open svs file in imageJ Best Regards, Yan ===================================== Yan Gao, Doctoral of Science, HTL (ASCP) Novartis Institutes for BioMedical Research _________________________ CONFIDENTIALITY NOTICE The information contained in this e-mail message is intended only for the exclusive use of the individual or entity named above and may contain information that is privileged, confidential or exempt from disclosure under applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivery of the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately by e-mail and delete the material from any computer. Thank you. |
|
|
In reply to this post by Yan Gao
>Can anyone tell me if I am able to open svs file in imageJ
Yan - I've heard from the vendor that the SVS files actually follows the TIF file format specification. When I've tried renaming an SVS file to a TIF file, it doesn't correctly open in ImageJ. When I try to open a renamed SVS with Photoshop, it opens correctly. I've never quite figured out why this is. I'm assuming that it's because they follow the TIF standard, but they may be using it in an unconventional way that not everyone supports. An even bigger issue, however, is the size of the SVS files. For my work, a typical SVS file is well over 10K x 20K (e.g., for an RGB image, file size is >600MB). The image analysis tools within the Aperio software get around this by analyzing chunks of a specified width & height (e.g., 1000 x 1000 pixel "tiles"). Here are what I think you're main options are: - You're best bet will be to export the images as TIF from ImageScope and then open them in ImageJ. - The next best option would be to see if someone on this list can help decipher why the SVS file isn't opening from within ImageJ. - A third option might be to work with Aperio to get their help creating an "analysis algorithm" for submitting images for analysis to ImageJ. In any of these cases, you will need to determine what the largest file size you can pass to ImageJ and do something to make sure that you're never passing anything larger to ImageJ (e.g., exporting specific sub-regions or using "tiling" to limit the file sizes). Jeff Hanson Senior Imaging Analyst Eli Lilly and Company [hidden email] |
Re: I would like doing image analysis of svs file by using imageJ
|
|
In reply to this post by Yan Gao
Hi Yan,
If you would be willing to send some files, we (LOCI) would be happy to add support for the SVS format to the LOCI Bio-Formats importer plugin ( http://www.loci.wisc.edu/ome/formats.html). If you need somewhere to put files, I can send you our FTP server information privately. Thanks and regards, -Melissa On Jan 4, 2008 1:55 PM, Yan Gao <[hidden email]> wrote: > Dear ImageJ: > I have a naive question for imageJ group. In our lab, we have Aperio > scanscope. The image file is svs file. The image analysis tools of > Aperio are limited. I would like do image analysis of these svs file by > using imageJ. Can anyone tell me if I am able to open svs file in imageJ > > > Best Regards, > > Yan > ===================================== > > Yan Gao, Doctoral of Science, HTL (ASCP) > Novartis Institutes for BioMedical Research > > > > > _________________________ > > CONFIDENTIALITY NOTICE > > The information contained in this e-mail message is intended only for the > exclusive use of the individual or entity named above and may contain > information that is privileged, confidential or exempt from disclosure > under applicable law. If the reader of this message is not the intended > recipient, or the employee or agent responsible for delivery of the > message to the intended recipient, you are hereby notified that any > dissemination, distribution or copying of this communication is strictly > prohibited. If you have received this communication in error, please > notify the sender immediately by e-mail and delete the material from any > computer. Thank you. > |
Re: ImageJ driving AVT Guppy CCD cam
|
|
In reply to this post by luc******
Hi Luc,
> I would like to interface my AVT Guppy CCD camera (see eg > http://www.firstsightvision.co.uk/cameras/avt-guppy.html) with > ImageJ for > grabbing images or image sequences. Does someone know whether it is The AVT Guppy cameras adhere to the iidc 1394 specs. This means that you could use Micro-manager with the IIDC adapter (http:// valelab.ucsf.edu/~nico/MMwiki/index.php/Dc1394), provided that: - the camera is monochrome (color will be supported in the upcoming Micro-Manager 1.2 release) - you run Mac or Linux - you use the firewire (IEEE 1394) interface, not USB 2.0. Best, Nico > possible, and if yes how to do? Are the Scion or the twain or any > other > packages helpful for that? > Many thanks... > -- > View this message in context: http://www.nabble.com/ImageJ-driving- > AVT-Guppy-CCD-cam-tp14401278p14401278.html > Sent from the ImageJ mailing list archive at Nabble.com. |
|
|
In reply to this post by Melissa Linkert
Hi, Melissa.
Thank you very much for your offer. Yes, I can send you some files. The files are too big, you need let me know how I can put the files in your server. I really appreciated your help. Best Regards, Yan ===================================== Yan Gao, Doctoral of Science, HTL (ASCP) Novartis Institutes for BioMedical Research Melissa Linkert <[hidden email]> Sent by: ImageJ Interest Group <[hidden email]> 01/04/2008 06:45 PM Please respond to ImageJ Interest Group <[hidden email]> To [hidden email] cc Subject Re: I would like doing image analysis of svs file by using imageJ Hi Yan, If you would be willing to send some files, we (LOCI) would be happy to add support for the SVS format to the LOCI Bio-Formats importer plugin ( http://www.loci.wisc.edu/ome/formats.html). If you need somewhere to put files, I can send you our FTP server information privately. Thanks and regards, -Melissa On Jan 4, 2008 1:55 PM, Yan Gao <[hidden email]> wrote: > Dear ImageJ: > I have a naive question for imageJ group. In our lab, we have Aperio > scanscope. The image file is svs file. The image analysis tools of > Aperio are limited. I would like do image analysis of these svs file by > using imageJ. Can anyone tell me if I am able to open svs file in imageJ > > > Best Regards, > > Yan > ===================================== > > Yan Gao, Doctoral of Science, HTL (ASCP) > Novartis Institutes for BioMedical Research > > > > > _________________________ > > CONFIDENTIALITY NOTICE > > The information contained in this e-mail message is intended only for > exclusive use of the individual or entity named above and may contain > information that is privileged, confidential or exempt from disclosure > under applicable law. If the reader of this message is not the intended > recipient, or the employee or agent responsible for delivery of the > message to the intended recipient, you are hereby notified that any > dissemination, distribution or copying of this communication is strictly > prohibited. If you have received this communication in error, please > notify the sender immediately by e-mail and delete the material from any > computer. Thank you. > _________________________ CONFIDENTIALITY NOTICE The information contained in this e-mail message is intended only for the exclusive use of the individual or entity named above and may contain information that is privileged, confidential or exempt from disclosure under applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivery of the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately by e-mail and delete the material from any computer. Thank you. |
Re: I would like doing image analysis of svs file by using imageJ
|
|
In reply to this post by Yan Gao
Melissa,
It would be great if we could get some an imageJ plugin for the Aperio file format. I would like to warn you somewhat about what you are getting into, though. As far as I understand it, the .svs file is a container format that can contain tiff, LZH compressed tiff, jpeg or jpeg2000 images. These are generally whole slide images and typically run around 120 MB per file for a 20x, highly compressed jpeg2000 image. That is somewhere around 1.5 gigapixels for a typical 20x slide. At 40x, the situation is even worse. So, there are really two issues with opening these files in imageJ. First,jpeg2000 (which b/c of image size, is the defacto default encoding for whole slide images) isn's supported by imageJ, although java libraries exist for handling the encoding. More concerning, is the massive size of these images. This will probably necessitate a lot of display tricks such as paging portions of the image into memory and using prescaled lower resolution images (included in the svs file) for zooming. I am not sure how much of this imageJ would support without a lot of new code or some serious hacks. Of course, I could be wrong and maybe large image support was added to imageJ at some point. So, I think adding .svs file support in considerably more than coding up import/export filters. That stated, there are MANY people that would love to see new tools for working with these files. The lock-in with Aperio is frustrating, especially when all of your analysis methods are imageJ-centric. If you are serious about getting some form of support for .svs files in imageJ as a plugin or otherwise, I would be glad to do whatever I could to aid you. toby > Date: Mon, 7 Jan 2008 14:01:44 -0500 > From: Yan Gao <[hidden email]> > Subject: Re: I would like doing image analysis of svs file by using imageJ > > Hi, Melissa. > > Thank you very much for your offer. Yes, I can send you some files. The > files are too big, you need let me know how I can put the files in your > server. I really appreciated your help. > > Best Regards, > > Yan >===================================== > >Yan Gao, Doctoral of Science, HTL (ASCP) >Novartis Institutes for BioMedical Research Toby C. Cornish, M.D., Ph.D. Pathology Resident Johns Hopkins Medical Institutions [hidden email] |
|
Hi Toby,
Thanks for the warning. Fortunately, Bio-Formats already supports nearly everything you mention in a modular fashion. It can already decode JPEG2000 using the JAI ImageIO tools library, works with JPEG and TIFF, including many forms of compressed TIFF (though we may need to code an LZH filter -- I don't think we handle LZH yet). To be perfectly clear: we are completely serious about Bio-Formats being a complete library for the exchange of microscopy data between both software packages and scientific organizations. We want to support conversion of every major microscopy file format, including both pixels and metadata, into a common data standard. As for the size of the image planes, Bio-Formats recently added an API for reading "sub-images" -- specific portions of an image plane within a bounding rectangle. So at worst, for gigantic image planes, the plugin will allow the user to specify a subregion to load in. If there is enough demand, we can add other sorts of "tile on import" types of functionality to the plugin as well. Depending on whether the planes are compressed as tiles, or as one gigantic compressed block, a large amount of system RAM may be required to read the files, but we have largely overcome the 2 GB (32-bit) RAM barrier at this point, so 1.5 gigapixels is becoming more manageable. Regarding improving ImageJ's support for working with huge images in general, that is something we can hopefully collaborate on with Wayne, since such functionality would be of wider applicability than just Aperio format. Ideally, Bio-Formats won't need any custom display logic, but rather ImageJ would have a "large image" mode that could be invoked, or something like that. The most useful thing people can do to help us in the immediate future would be to send us some SVS samples. Ideally, we would have one or more samples in each of the internal formats within the container (i.e., one in JPEG2000, one JPEG, one TIFF, one TIFF-LZH, etc.). If you can provide download links to some samples, that would be great. Otherwise, if you need a place to upload files, I can send you our FTP information privately -- just let me know. This same offer goes for ANY file format people would like to see added to Bio-Formats -- send us some sample data, and we will do our best to add support for the format, as time allows. Depending on the complexity of the format, I cannot promise a particular time frame, but most formats end up being pretty simple to add, so chances are good we can do it reasonably quickly. -Curtis On Jan 9, 2008 12:13 AM, Toby Cornish <[hidden email]> wrote: > Melissa, > > It would be great if we could get some an imageJ plugin for the Aperio file format. I would like to warn you somewhat about what you are getting into, though. As far as I understand it, the .svs file is a container format that can contain tiff, LZH compressed tiff, jpeg or jpeg2000 images. These are generally whole slide images and typically run around 120 MB per file for a 20x, highly compressed jpeg2000 image. That is somewhere around 1.5 gigapixels for a typical 20x slide. At 40x, the situation is even worse. > > So, there are really two issues with opening these files in imageJ. First,jpeg2000 (which b/c of image size, is the defacto default encoding for whole slide images) isn's supported by imageJ, although java libraries exist for handling the encoding. More concerning, is the massive size of these images. This will probably necessitate a lot of display tricks such as paging portions of the image into memory and using prescaled lower resolution images (included in the svs file) for zooming. I am not sure how much of this imageJ would support without a lot of new code or some serious hacks. Of course, I could be wrong and maybe large image support was added to imageJ at some point. > > So, I think adding .svs file support in considerably more than coding up import/export filters. That stated, there are MANY people that would love to see new tools for working with these files. The lock-in with Aperio is frustrating, especially when all of your analysis methods are imageJ-centric. If you are serious about getting some form of support for .svs files in imageJ as a plugin or otherwise, I would be glad to do whatever I could to aid you. > > toby > > > > > Date: Mon, 7 Jan 2008 14:01:44 -0500 > > From: Yan Gao <[hidden email]> > > Subject: Re: I would like doing image analysis of svs file by using imageJ > > > > Hi, Melissa. > > > > Thank you very much for your offer. Yes, I can send you some files. The > > files are too big, you need let me know how I can put the files in your > > server. I really appreciated your help. > > > > Best Regards, > > > > Yan > >===================================== > > > >Yan Gao, Doctoral of Science, HTL (ASCP) > >Novartis Institutes for BioMedical Research > > > Toby C. Cornish, M.D., Ph.D. > Pathology Resident > Johns Hopkins Medical Institutions > [hidden email] > |
|
|
In reply to this post by Nico Stuurman-4
Hi Nico,
thanks a lot for your answer. What happens if i run Windows?... Best, Luc
|
«
Return to ImageJ
|
1 view|%1 views
| Free forum by Nabble | Edit this page |