Section View
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Dear All,
I sent a message recently regarding whether anyone knew a way of generating a section view such as you can do with the Leica SP2 confocal software. I have put a section view image on our website at: http://www.health.auckland.ac.nz/biru/exptal_images/index.html to show what I am trying to achieve. We have an older confocal microscope where we can do z series and projections, etc. but can't generate the section view. I have tried using BioimageXD but it doesn't seem to want to combine the two channels. If anyone can help me with this, either using ImageJ or another freeware, that would be much appreciated. Cheers, Jacqui. Jacqueline Ross Biomedical Imaging Research Unit Department of Anatomy with Radiology Faculty of Medical & Health Sciences The University of Auckland Private Bag 92019 Auckland, NEW ZEALAND Tel: 64 9 373 7599 Ext 87438 Fax: 64 9 373 7484 http://www.health.auckland.ac.nz/biru/ <http://www.health.auckland.ac.nz/biru/> |
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Dear Jacqui,
did you already try the 3D Volume Viewer? You can have a view of x-y, y-z, x-z. It is not arranged as you show it on your internet page. But it gives you the section view you are asking for. The z-aspect allows you to arrange the height of your z-view. Anneliese Jacqui Ross schrieb: >Dear All, > > > >I sent a message recently regarding whether anyone knew a way of >generating a section view such as you can do with the Leica SP2 confocal >software. > > > >I have put a section view image on our website at: >http://www.health.auckland.ac.nz/biru/exptal_images/index.html to show >what I am trying to achieve. > > > >We have an older confocal microscope where we can do z series and >projections, etc. but can't generate the section view. > > > >I have tried using BioimageXD but it doesn't seem to want to combine the >two channels. > > > >If anyone can help me with this, either using ImageJ or another >freeware, that would be much appreciated. > > > >Cheers, > > > >Jacqui. > > > >Jacqueline Ross >Biomedical Imaging Research Unit >Department of Anatomy with Radiology >Faculty of Medical & Health Sciences >The University of Auckland >Private Bag 92019 >Auckland, NEW ZEALAND > >Tel: 64 9 373 7599 Ext 87438 >Fax: 64 9 373 7484 > >http://www.health.auckland.ac.nz/biru/ ><http://www.health.auckland.ac.nz/biru/> > > > > > |
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In reply to this post by Jacqueline Ross
Dear Anneliese,
Thanks very much for your reply. I had tried the Volume Viewer but didn't realise what the z aspect adjustment was for. I tried it just now and it looks like what I am looking for now that I am adjusting the z aspect to about 4. Can you tell me how the z aspect adjustment is working? Is it just spacing out the data set? In which case, should I put in the value that I know is correct in pixels/microns (step size) or isn't it really necessary? Thanks again, Cheers, Jacqui. Jacqueline Ross Biomedical Imaging Research Unit Department of Anatomy with Radiology Faculty of Medical & Health Sciences The University of Auckland Private Bag 92019 Auckland, NEW ZEALAND Tel: 64 9 373 7599 Ext 87438 Fax: 64 9 373 7484 http://www.health.auckland.ac.nz/biru/ -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Klughammer GmbH Sent: 02 June 2006 18:14 To: [hidden email] Subject: Re: Section View Dear Jacqui, did you already try the 3D Volume Viewer? You can have a view of x-y, y-z, x-z. It is not arranged as you show it on your internet page. But it gives you the section view you are asking for. The z-aspect allows you to arrange the height of your z-view. Anneliese Jacqui Ross schrieb: >Dear All, > > > >I sent a message recently regarding whether anyone knew a way of >generating a section view such as you can do with the Leica SP2 confocal >software. > > > >I have put a section view image on our website at: >http://www.health.auckland.ac.nz/biru/exptal_images/index.html to show >what I am trying to achieve. > > > >We have an older confocal microscope where we can do z series and >projections, etc. but can't generate the section view. > > > >I have tried using BioimageXD but it doesn't seem to want to combine >two channels. > > > >If anyone can help me with this, either using ImageJ or another >freeware, that would be much appreciated. > > > >Cheers, > > > >Jacqui. > > > >Jacqueline Ross >Biomedical Imaging Research Unit >Department of Anatomy with Radiology >Faculty of Medical & Health Sciences >The University of Auckland >Private Bag 92019 >Auckland, NEW ZEALAND > >Tel: 64 9 373 7599 Ext 87438 >Fax: 64 9 373 7484 > >http://www.health.auckland.ac.nz/biru/ ><http://www.health.auckland.ac.nz/biru/> > > > > > |
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Dear Jacqui,
I cannot tell you more about the z-aspect adjustment. It was written by Kai Uwe Barthel (k.barthel at fhtw-berlin.de). On the web page http://rsb.info.nih.gov/ij/plugins/volume-viewer.html you can read that "The *z-aspect *ratio is read automatically, but it can also be set". Maybe he can tell us more about it which would be interesting to all of us who use this plug-in. Anneliese Jacqui Ross schrieb: >Dear Anneliese, > >Thanks very much for your reply. I had tried the Volume Viewer but >didn't realise what the z aspect adjustment was for. I tried it just now >and it looks like what I am looking for now that I am adjusting the z >aspect to about 4. > >Can you tell me how the z aspect adjustment is working? Is it just >spacing out the data set? In which case, should I put in the value that >I know is correct in pixels/microns (step size) or isn't it really >necessary? > >Thanks again, > >Cheers, > >Jacqui. > >Jacqueline Ross >Biomedical Imaging Research Unit >Department of Anatomy with Radiology >Faculty of Medical & Health Sciences >The University of Auckland >Private Bag 92019 >Auckland, NEW ZEALAND > >Tel: 64 9 373 7599 Ext 87438 >Fax: 64 9 373 7484 > >http://www.health.auckland.ac.nz/biru/ >-----Original Message----- >From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of >Klughammer GmbH >Sent: 02 June 2006 18:14 >To: [hidden email] >Subject: Re: Section View > >Dear Jacqui, > >did you already try the 3D Volume Viewer? You can have a view of x-y, >y-z, x-z. It is not arranged as you show it on your internet page. But >it gives you the section view you are asking for. The z-aspect allows >you to arrange the height of your z-view. > >Anneliese > > >Jacqui Ross schrieb: > > > >>Dear All, >> >> >> >>I sent a message recently regarding whether anyone knew a way of >>generating a section view such as you can do with the Leica SP2 >> >> >confocal > > >>software. >> >> >> >>I have put a section view image on our website at: >>http://www.health.auckland.ac.nz/biru/exptal_images/index.html to show >>what I am trying to achieve. >> >> >> >>We have an older confocal microscope where we can do z series and >>projections, etc. but can't generate the section view. >> >> >> >>I have tried using BioimageXD but it doesn't seem to want to combine >> >> >the > > >>two channels. >> >> >> >>If anyone can help me with this, either using ImageJ or another >>freeware, that would be much appreciated. >> >> >> >>Cheers, >> >> >> >>Jacqui. >> >> >> >>Jacqueline Ross >>Biomedical Imaging Research Unit >>Department of Anatomy with Radiology >>Faculty of Medical & Health Sciences >>The University of Auckland >>Private Bag 92019 >>Auckland, NEW ZEALAND >> >>Tel: 64 9 373 7599 Ext 87438 >>Fax: 64 9 373 7484 >> >>http://www.health.auckland.ac.nz/biru/ >><http://www.health.auckland.ac.nz/biru/> >> >> >> >> >> >> >> > > > |
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In reply to this post by Jacqueline Ross
Dear Anneliese,
Thanks for the additional information about the z aspect. If the writer doesn't write to the list, I will try contacting him for clarification. If I get anything useful, I will let you know. Thanks again. Cheers, Jacqui. Jacqueline Ross Biomedical Imaging Research Unit Department of Anatomy with Radiology Faculty of Medical & Health Sciences The University of Auckland Private Bag 92019 Auckland, NEW ZEALAND Tel: 64 9 373 7599 Ext 87438 Fax: 64 9 373 7484 http://www.health.auckland.ac.nz/biru/ -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Klughammer GmbH Sent: 02 June 2006 18:54 To: [hidden email] Subject: Re: Section View Dear Jacqui, I cannot tell you more about the z-aspect adjustment. It was written by Kai Uwe Barthel (k.barthel at fhtw-berlin.de). On the web page http://rsb.info.nih.gov/ij/plugins/volume-viewer.html you can read that "The *z-aspect *ratio is read automatically, but it can also be set". Maybe he can tell us more about it which would be interesting to all of us who use this plug-in. Anneliese Jacqui Ross schrieb: >Dear Anneliese, > >Thanks very much for your reply. I had tried the Volume Viewer but >didn't realise what the z aspect adjustment was for. I tried it just now >and it looks like what I am looking for now that I am adjusting the z >aspect to about 4. > >Can you tell me how the z aspect adjustment is working? Is it just >spacing out the data set? In which case, should I put in the value that >I know is correct in pixels/microns (step size) or isn't it really >necessary? > >Thanks again, > >Cheers, > >Jacqui. > >Jacqueline Ross >Biomedical Imaging Research Unit >Department of Anatomy with Radiology >Faculty of Medical & Health Sciences >The University of Auckland >Private Bag 92019 >Auckland, NEW ZEALAND > >Tel: 64 9 373 7599 Ext 87438 >Fax: 64 9 373 7484 > >http://www.health.auckland.ac.nz/biru/ >-----Original Message----- >From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of >Klughammer GmbH >Sent: 02 June 2006 18:14 >To: [hidden email] >Subject: Re: Section View > >Dear Jacqui, > >did you already try the 3D Volume Viewer? You can have a view of x-y, >y-z, x-z. It is not arranged as you show it on your internet page. But >it gives you the section view you are asking for. The z-aspect allows >you to arrange the height of your z-view. > >Anneliese > > >Jacqui Ross schrieb: > > > >>Dear All, >> >> >> >>I sent a message recently regarding whether anyone knew a way of >>generating a section view such as you can do with the Leica SP2 >> >> >confocal > > >>software. >> >> >> >>I have put a section view image on our website at: >>http://www.health.auckland.ac.nz/biru/exptal_images/index.html to show >>what I am trying to achieve. >> >> >> >>We have an older confocal microscope where we can do z series and >>projections, etc. but can't generate the section view. >> >> >> >>I have tried using BioimageXD but it doesn't seem to want to combine >> >> >the > > >>two channels. >> >> >> >>If anyone can help me with this, either using ImageJ or another >>freeware, that would be much appreciated. >> >> >> >>Cheers, >> >> >> >>Jacqui. >> >> >> >>Jacqueline Ross >>Biomedical Imaging Research Unit >>Department of Anatomy with Radiology >>Faculty of Medical & Health Sciences >>The University of Auckland >>Private Bag 92019 >>Auckland, NEW ZEALAND >> >>Tel: 64 9 373 7599 Ext 87438 >>Fax: 64 9 373 7484 >> >>http://www.health.auckland.ac.nz/biru/ >><http://www.health.auckland.ac.nz/biru/> >> >> >> >> >> >> >> > > > |
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Dear Jacqui,
I am not sure it exactly what you are looking for but have you consider using ImageSurfer? Freeware available at: http://152.19.37.82/ /LAurent ______________________________________________ Laurent Barbe, Research Fellow Royal University of Technology (KTH) School of Nanobiotechnology - Dpt of Biotechnology Roslagstullsbacken 21, 10601 STOCKHOLM SWEDEN Tel: (+46) 855378832 Fax: (+46) 855378323 -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Jacqui Ross Sent: tisdag 6 juni 2006 00:49 To: [hidden email] Subject: Re: Section View Dear Anneliese, Thanks for the additional information about the z aspect. If the writer doesn't write to the list, I will try contacting him for clarification. If I get anything useful, I will let you know. Thanks again. Cheers, Jacqui. Jacqueline Ross Biomedical Imaging Research Unit Department of Anatomy with Radiology Faculty of Medical & Health Sciences The University of Auckland Private Bag 92019 Auckland, NEW ZEALAND Tel: 64 9 373 7599 Ext 87438 Fax: 64 9 373 7484 http://www.health.auckland.ac.nz/biru/ -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Klughammer GmbH Sent: 02 June 2006 18:54 To: [hidden email] Subject: Re: Section View Dear Jacqui, I cannot tell you more about the z-aspect adjustment. It was written by Kai Uwe Barthel (k.barthel at fhtw-berlin.de). On the web page http://rsb.info.nih.gov/ij/plugins/volume-viewer.html you can read that "The *z-aspect *ratio is read automatically, but it can also be set". Maybe he can tell us more about it which would be interesting to all of us who use this plug-in. Anneliese Jacqui Ross schrieb: >Dear Anneliese, > >Thanks very much for your reply. I had tried the Volume Viewer but >didn't realise what the z aspect adjustment was for. I tried it just now >and it looks like what I am looking for now that I am adjusting the z >aspect to about 4. > >Can you tell me how the z aspect adjustment is working? Is it just >spacing out the data set? In which case, should I put in the value that >I know is correct in pixels/microns (step size) or isn't it really >necessary? > >Thanks again, > >Cheers, > >Jacqui. > >Jacqueline Ross >Biomedical Imaging Research Unit >Department of Anatomy with Radiology >Faculty of Medical & Health Sciences >The University of Auckland >Private Bag 92019 >Auckland, NEW ZEALAND > >Tel: 64 9 373 7599 Ext 87438 >Fax: 64 9 373 7484 > >http://www.health.auckland.ac.nz/biru/ >-----Original Message----- >From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of >Klughammer GmbH >Sent: 02 June 2006 18:14 >To: [hidden email] >Subject: Re: Section View > >Dear Jacqui, > >did you already try the 3D Volume Viewer? You can have a view of x-y, >y-z, x-z. It is not arranged as you show it on your internet page. But >it gives you the section view you are asking for. The z-aspect allows >you to arrange the height of your z-view. > >Anneliese > > >Jacqui Ross schrieb: > > > >>Dear All, >> >> >> >>I sent a message recently regarding whether anyone knew a way of >>generating a section view such as you can do with the Leica SP2 >> >> >confocal > > >>software. >> >> >> >>I have put a section view image on our website at: >>http://www.health.auckland.ac.nz/biru/exptal_images/index.html to show >>what I am trying to achieve. >> >> >> >>We have an older confocal microscope where we can do z series and >>projections, etc. but can't generate the section view. >> >> >> >>I have tried using BioimageXD but it doesn't seem to want to combine >> >> >the > > >>two channels. >> >> >> >>If anyone can help me with this, either using ImageJ or another >>freeware, that would be much appreciated. >> >> >> >>Cheers, >> >> >> >>Jacqui. >> >> >> >>Jacqueline Ross >>Biomedical Imaging Research Unit >>Department of Anatomy with Radiology >>Faculty of Medical & Health Sciences >>The University of Auckland >>Private Bag 92019 >>Auckland, NEW ZEALAND >> >>Tel: 64 9 373 7599 Ext 87438 >>Fax: 64 9 373 7484 >> >>http://www.health.auckland.ac.nz/biru/ >><http://www.health.auckland.ac.nz/biru/> >> >> >> >> >> >> >> > > > |
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In reply to this post by Jacqueline Ross
Dear Laurent,
Thanks very much for the link to ImageSurfer. I have to admit that I hadn't heard of this program. However, it does look quite interesting and worth looking into especially for 3D judging by the images on the homepage. Cheers, Jacqui. Jacqueline Ross Biomedical Imaging Research Unit Department of Anatomy with Radiology Faculty of Medical & Health Sciences The University of Auckland Private Bag 92019 Auckland, NEW ZEALAND Tel: 64 9 373 7599 Ext 87438 Fax: 64 9 373 7484 http://www.health.auckland.ac.nz/biru/ -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of laurent barbe Sent: 07 June 2006 21:39 To: [hidden email] Subject: Re: Section View Dear Jacqui, I am not sure it exactly what you are looking for but have you consider using ImageSurfer? Freeware available at: http://152.19.37.82/ /LAurent ______________________________________________ Laurent Barbe, Research Fellow Royal University of Technology (KTH) School of Nanobiotechnology - Dpt of Biotechnology Roslagstullsbacken 21, 10601 STOCKHOLM SWEDEN Tel: (+46) 855378832 Fax: (+46) 855378323 -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Jacqui Ross Sent: tisdag 6 juni 2006 00:49 To: [hidden email] Subject: Re: Section View Dear Anneliese, Thanks for the additional information about the z aspect. If the writer doesn't write to the list, I will try contacting him for clarification. If I get anything useful, I will let you know. Thanks again. Cheers, Jacqui. Jacqueline Ross Biomedical Imaging Research Unit Department of Anatomy with Radiology Faculty of Medical & Health Sciences The University of Auckland Private Bag 92019 Auckland, NEW ZEALAND Tel: 64 9 373 7599 Ext 87438 Fax: 64 9 373 7484 http://www.health.auckland.ac.nz/biru/ -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Klughammer GmbH Sent: 02 June 2006 18:54 To: [hidden email] Subject: Re: Section View Dear Jacqui, I cannot tell you more about the z-aspect adjustment. It was written by Kai Uwe Barthel (k.barthel at fhtw-berlin.de). On the web page http://rsb.info.nih.gov/ij/plugins/volume-viewer.html you can read that "The *z-aspect *ratio is read automatically, but it can also be set". Maybe he can tell us more about it which would be interesting to all of us who use this plug-in. Anneliese Jacqui Ross schrieb: >Dear Anneliese, > >Thanks very much for your reply. I had tried the Volume Viewer but >didn't realise what the z aspect adjustment was for. I tried it just now >and it looks like what I am looking for now that I am adjusting the z >aspect to about 4. > >Can you tell me how the z aspect adjustment is working? Is it just >spacing out the data set? In which case, should I put in the value that >I know is correct in pixels/microns (step size) or isn't it really >necessary? > >Thanks again, > >Cheers, > >Jacqui. > >Jacqueline Ross >Biomedical Imaging Research Unit >Department of Anatomy with Radiology >Faculty of Medical & Health Sciences >The University of Auckland >Private Bag 92019 >Auckland, NEW ZEALAND > >Tel: 64 9 373 7599 Ext 87438 >Fax: 64 9 373 7484 > >http://www.health.auckland.ac.nz/biru/ >-----Original Message----- >From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of >Klughammer GmbH >Sent: 02 June 2006 18:14 >To: [hidden email] >Subject: Re: Section View > >Dear Jacqui, > >did you already try the 3D Volume Viewer? You can have a view of x-y, >y-z, x-z. It is not arranged as you show it on your internet page. But >it gives you the section view you are asking for. The z-aspect allows >you to arrange the height of your z-view. > >Anneliese > > >Jacqui Ross schrieb: > > > >>Dear All, >> >> >> >>I sent a message recently regarding whether anyone knew a way of >>generating a section view such as you can do with the Leica SP2 >> >> >confocal > > >>software. >> >> >> >>I have put a section view image on our website at: >>http://www.health.auckland.ac.nz/biru/exptal_images/index.html to show >>what I am trying to achieve. >> >> >> >>We have an older confocal microscope where we can do z series and >>projections, etc. but can't generate the section view. >> >> >> >>I have tried using BioimageXD but it doesn't seem to want to combine >> >> >the > > >>two channels. >> >> >> >>If anyone can help me with this, either using ImageJ or another >>freeware, that would be much appreciated. >> >> >> >>Cheers, >> >> >> >>Jacqui. >> >> >> >>Jacqueline Ross >>Biomedical Imaging Research Unit >>Department of Anatomy with Radiology >>Faculty of Medical & Health Sciences >>The University of Auckland >>Private Bag 92019 >>Auckland, NEW ZEALAND >> >>Tel: 64 9 373 7599 Ext 87438 >>Fax: 64 9 373 7484 >> >>http://www.health.auckland.ac.nz/biru/ >><http://www.health.auckland.ac.nz/biru/> >> >> >> >> >> >> >> > > > |
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