Micro-Manager with Axiophot2
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simon walker (BI) |
Micro-Manager with Axiophot2
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** Ok, so this isn't a confocal question, but I was wondering if anyone has any experience or suggestions with this. I'm trying to get a Hamamatsu ORCA camera to run on a Zeiss Axioplan2/Axiophot2 microscope using Micro- Manager. I can get the camera to work, but I have failed to get the microscope to work (port switching is computer controlled). I can't get the software to recognise the microscope - I keep getting a com error when the software attempts to load the ZeissCAN adapter. I know there is nothing wrong with the microscope (it runs fine using the original Zeiss software under Win98, but the camera does not) and there is nothing wrong with the pc (I get the same error with different pcs). Can anyone suggest what I might be doing wrong, or is it just a case of Micro-Manager not supporting the Axiophot2? Is there any other free software that could potentially drive an ORCA camera and an Axiophot2? Thanks, Simon Babraham Institute UK |
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** Dear All, I'm sorry for the off-topic enquiry. However, if anyone has a lot of experience with the visualisation program Amira, I would really appreciate hearing from you. Thanks! 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, NEW ZEALAND Tel: 64 9 373 7599 Ext 87438 Fax: 64 9 373 7484 http://www.fmhs.auckland.ac.nz/sms/biru/ |
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** Hi Jacqui, On Oct 20, 2010, at 7:01 AM, CONFOCALMICROSCOPY automatic digest system wrote: > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=3Dconfocalmicroscopy > ***** > > Dear All, > > I'm sorry for the off-topic enquiry. However, if anyone has a lot of > experience with the visualisation program Amira, I would really > appreciate hearing from you. Its got some nice features but its very expensive, and comes with the usual support and license problems of proprietary software, and they will never tell you exactly how it works as they wantt o protect their "intellectual property" so its hard to really know what your results mean sometimes. I am biased... I help develop open source software for microscopy, but there is really not much that Amira can do that ImageJ (Fiji distro) and BioImageXD can do for 0 dollars plus some user feedback in return. You are better off using the money to hire a masters level programmer to make custom plugins and solutions for you that can also be shared with the community using a GPL license. For an academic situation this is much better. Better bang per buck. my 2 c Dan > > Thanks! > > Kind regards, > > Jacqui > > Jacqueline Ross=20 > > Biomedical Imaging Microscopist > Biomedical Imaging Research Unit=20 > School of Medical Sciences=20 > Faculty of Medical & Health Sciences=20 > The University of Auckland=20 > Private Bag 92019=20 > Auckland, NEW ZEALAND=20 > > Tel: 64 9 373 7599 Ext 87438=20 > Fax: 64 9 373 7484=20 > > http://www.fmhs.auckland.ac.nz/sms/biru/ Dr. Daniel James White BSc. (Hons.) PhD Senior Microscopist / Image Visualisation, Processing and Analysis Light Microscopy and Image Processing Facilities Max Planck Institute of Molecular Cell Biology and Genetics Pfotenhauerstrasse 108 01307 DRESDEN Germany +49 (0)15114966933 (German Mobile) +49 (0)351 210 2627 (Work phone at MPI-CBG) +49 (0)351 210 1078 (Fax MPI-CBG LMF) http://www.bioimagexd.net BioImageXD http://pacific.mpi-cbg.de Fiji - is just ImageJ (Batteries Included) http://www.chalkie.org.uk Dan's Homepages https://ifn.mpi-cbg.de Dresden Imaging Facility Network dan (at) chalkie.org.uk ( white (at) mpi-cbg.de ) |
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** I fully agree with Daniel - this is just what I've done for our facility here: Open source & customisation where required. And the training to go with it, to bypass certain slightly awkward and not-so-user-friendly aspects (user-friendliness is somewhat overrated and highly subjective anyway, methinks). Philippe On Wed, Oct 20, 2010 at 8:59 AM, Daniel James White <[hidden email]>wrote: > ***** > To join, leave or search the confocal microscopy listserv, go to: > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy > ***** > > Hi Jacqui, > > On Oct 20, 2010, at 7:01 AM, CONFOCALMICROSCOPY automatic digest system > wrote: > > > ***** > > To join, leave or search the confocal microscopy listserv, go to: > > http://lists.umn.edu/cgi-bin/wa?A0=3Dconfocalmicroscopy > > ***** > > > > Dear All, > > > > I'm sorry for the off-topic enquiry. However, if anyone has a lot of > > experience with the visualisation program Amira, I would really > > appreciate hearing from you. > > > Its got some nice features but its very expensive, > and comes with the usual support and license problems of proprietary > software, > and they will never tell you exactly how it works as they wantt o protect > their "intellectual property" > so its hard to really know what your results mean sometimes. > > I am biased... I help develop open source software for microscopy, > but there is really not much that Amira can do that > ImageJ (Fiji distro) and BioImageXD can do for 0 dollars plus some user > feedback in return. > > You are better off using the money to hire a masters level programmer to > make custom plugins and solutions > for you that can also be shared with the community using a GPL license. > > For an academic situation this is much better. > > Better bang per buck. > > my 2 c > > Dan > > > > > > > Thanks! > > > > Kind regards, > > > > Jacqui > > > > Jacqueline Ross=20 > > > > Biomedical Imaging Microscopist > > Biomedical Imaging Research Unit=20 > > School of Medical Sciences=20 > > Faculty of Medical & Health Sciences=20 > > The University of Auckland=20 > > Private Bag 92019=20 > > Auckland, NEW ZEALAND=20 > > > > Tel: 64 9 373 7599 Ext 87438=20 > > Fax: 64 9 373 7484=20 > > > > http://www.fmhs.auckland.ac.nz/sms/biru/ > > Dr. Daniel James White BSc. (Hons.) PhD > Senior Microscopist / Image Visualisation, Processing and Analysis > Light Microscopy and Image Processing Facilities > Max Planck Institute of Molecular Cell Biology and Genetics > Pfotenhauerstrasse 108 > 01307 DRESDEN > Germany > > +49 (0)15114966933 (German Mobile) > +49 (0)351 210 2627 (Work phone at MPI-CBG) > +49 (0)351 210 1078 (Fax MPI-CBG LMF) > > http://www.bioimagexd.net BioImageXD > http://pacific.mpi-cbg.de Fiji - is just ImageJ (Batteries > Included) > http://www.chalkie.org.uk Dan's Homepages > https://ifn.mpi-cbg.de Dresden Imaging Facility Network > dan (at) chalkie.org.uk > ( white (at) mpi-cbg.de ) > |
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** > > > Dear All, > > > > > > I'm sorry for the off-topic enquiry. However, if anyone has a lot of > > > experience with the visualisation program Amira, I would really > > > appreciate hearing from you. I think downloading the trial versions of the different packages and doing the tutorials (!) is always a good idea. This might take a few days but you will have to do it anyway with the software you decide do use... The Amira user interface is different from other packages but quite simple if you know what to do. What do you want to do with the software exactly? As long as you have well aligned stacks everything is nice, but a 3D reconstruction from thousands of single images of semi-thin sections can be quite frustrating... ;-) Torsten |
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** Dear All, Thanks Torsten, Dan and Phil for your comments and advice. Thanks also to Jen, who I have now been in contact with and she has already offered some suggestions. We actually already have the program, which we purchased about 5 years ago initially to support our electron microscope for tomographic reconstruction, etc. I guess I should have mentioned that in my email so I'm sorry about that. We have also used it quite a lot for reconstruction of CT and MRI scans, which it does superbly. So, since we found that the visualisation capabilities of the program were really good we subsequently upgraded to version 5 and now have additional licences but are having quite a few issues with crashing so I'm trying to contact other users to see if they have had similar experiences and can offer some suggestions with regard to solutions. We are also in contact with Visage Tech Support but sometimes users have a better idea of what our issues are since they can be data-related too. So, at the moment, I'm unsure of whether our issues are hardware or software-related. We have the MESH pack, microscopy (including deconvolution) and quantification modules so having made the investment, we really want to get them working reliably with our microscopy data, which is generally more complicated than CT, etc. I do support Dan's comments with regard to open source and freeware. I have also used BioImageXD a lot in the past although not so much recently. I am an absolute fan of ImageJ and use that program with Plugins, etc. a lot and it is the program I recommend the most to our users, not only because they can install on their own computers, but also because of the apparent simplicity (which is less intimidating) and great support from the user community. Anyway, sorry about taking the listserver off track! If anyone else has experience with Amira, I would really appreciate hearing from you. You are welcome to write to me off-list. 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, NEW ZEALAND Tel: 64 9 373 7599 Ext 87438 Fax: 64 9 373 7484 http://www.fmhs.auckland.ac.nz/sms/biru/ -----Original Message----- From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of [hidden email] Sent: Wednesday, 20 October 2010 11:31 p.m. To: [hidden email] Subject: Re: Off topic - Amira ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** > > > Dear All, > > > > > > I'm sorry for the off-topic enquiry. However, if anyone has a lot of > > > experience with the visualisation program Amira, I would really > > > appreciate hearing from you. I think downloading the trial versions of the different packages and doing the tutorials (!) is always a good idea. This might take a few days but you will have to do it anyway with the software you decide do use... The Amira user interface is different from other packages but quite simple if you know what to do. What do you want to do with the software exactly? As long as you have well aligned stacks everything is nice, but a 3D reconstruction from thousands of single images of semi-thin sections can be quite frustrating... ;-) Torsten |
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** +++++Commercial Posting+++++ Hello Confocal List Members I would like to invite you to attend our upcoming online seminar: Light Microscopy Fundamentals Presented by Paul Goodwin Technical Fellow & Director of Advanced Applications Applied Precision, Inc November 3, 2010 at the following times: 6 a.m., 11 a.m., and 6 p.m. PST The light microscope is one of the most important tools in biology. This webinar will cover image formation in the light microscope and discuss the essential elements of the light microscope - magnification, resolution, and contrast. We will also cover how aberrations impact contrast and resolution and discuss methods to assess optical performance. We will then discuss the relationship of sample preparation, the optical pathway and the microscope in its entirety. We will finish with practical recommendations for obtaining the best performance out of your microscope and the best data from your microscopy-based experiments. Sign up online at http://www.apiwebinars.webex.com Ian Clements Product Manager - DeltaVision OMX Systems This email message, together with any attachments, is for the sole use of the intended recipient(s) and is the confidential information of Applied Precision Inc. If you are not the intended recipient, your review, use, disclosure, copying or dissemination of this email message or its attachments, or the information contained therein, is strictly prohibited. If you are not the intended recipient or if you think this email was sent to you in error, please notify the sender by reply email and delete this message and its attachments, as well as all copies, from your system. |
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Hi Ian, I am setting up the seminar room for the webinar for next week, is there going to be any interaction with the audience? Q and A s etc?
Kind Regards, Grace Grace Chojnowski Flow Cytometry and Confocal Microscopy Laboratory Manager Queensland Institute of Medical Research Brisbane, QLD, AUSTRALIA [hidden email] +61 7 3362 0314. 6+61 414 956 752 +61 7 3362 0107 http://www.qimr.edu.au/flow -----Original Message----- From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Clements, Ian Sent: Friday, 22 October 2010 8:28 AM To: [hidden email] Subject: Re: Vendor Webinar ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** +++++Commercial Posting+++++ Hello Confocal List Members I would like to invite you to attend our upcoming online seminar: Light Microscopy Fundamentals Presented by Paul Goodwin Technical Fellow & Director of Advanced Applications Applied Precision, Inc November 3, 2010 at the following times: 6 a.m., 11 a.m., and 6 p.m. PST The light microscope is one of the most important tools in biology. This webinar will cover image formation in the light microscope and discuss the essential elements of the light microscope - magnification, resolution, and contrast. We will also cover how aberrations impact contrast and resolution and discuss methods to assess optical performance. We will then discuss the relationship of sample preparation, the optical pathway and the microscope in its entirety. We will finish with practical recommendations for obtaining the best performance out of your microscope and the best data from your microscopy-based experiments. Sign up online at http://www.apiwebinars.webex.com Ian Clements Product Manager - DeltaVision OMX Systems This email message, together with any attachments, is for the sole use of the intended recipient(s) and is the confidential information of Applied Precision Inc. If you are not the intended recipient, your review, use, disclosure, copying or dissemination of this email message or its attachments, or the information contained therein, is strictly prohibited. If you are not the intended recipient or if you think this email was sent to you in error, please notify the sender by reply email and delete this message and its attachments, as well as all copies, from your system. |
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The "sign up" link does not work, at least from France. I have several colleagues interrested in such a webminar. How can we sign up? Thanks Sandrine ________________________________________ De : Confocal Microscopy List [[hidden email]] de la part de Grace Chojnowski [[hidden email]] Date d'envoi : jeudi 28 octobre 2010 01:54 À : [hidden email] Objet : Re: Vendor Webinar Hi Ian, I am setting up the seminar room for the webinar for next week, is there going to be any interaction with the audience? Q and A s etc? Kind Regards, Grace Grace Chojnowski Flow Cytometry and Confocal Microscopy Laboratory Manager Queensland Institute of Medical Research Brisbane, QLD, AUSTRALIA [hidden email] +61 7 3362 0314. 6+61 414 956 752 +61 7 3362 0107 http://www.qimr.edu.au/flow -----Original Message----- From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Clements, Ian Sent: Friday, 22 October 2010 8:28 AM To: [hidden email] Subject: Re: Vendor Webinar ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** +++++Commercial Posting+++++ Hello Confocal List Members I would like to invite you to attend our upcoming online seminar: Light Microscopy Fundamentals Presented by Paul Goodwin Technical Fellow & Director of Advanced Applications Applied Precision, Inc November 3, 2010 at the following times: 6 a.m., 11 a.m., and 6 p.m. PST The light microscope is one of the most important tools in biology. This webinar will cover image formation in the light microscope and discuss the essential elements of the light microscope - magnification, resolution, and contrast. We will also cover how aberrations impact contrast and resolution and discuss methods to assess optical performance. We will then discuss the relationship of sample preparation, the optical pathway and the microscope in its entirety. We will finish with practical recommendations for obtaining the best performance out of your microscope and the best data from your microscopy-based experiments. Sign up online at http://www.apiwebinars.webex.com Ian Clements Product Manager - DeltaVision OMX Systems This email message, together with any attachments, is for the sole use of the intended recipient(s) and is the confidential information of Applied Precision Inc. If you are not the intended recipient, your review, use, disclosure, copying or dissemination of this email message or its attachments, or the information contained therein, is strictly prohibited. If you are not the intended recipient or if you think this email was sent to you in error, please notify the sender by reply email and delete this message and its attachments, as well as all copies, from your system. |
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** Sorry for the confusion, but the correct link is: http://apiwebinars.webex.com Tom -----Original Message----- From: POUVREAU SANDRINE [mailto:[hidden email]] Sent: Saturday, October 30, 2010 8:54 AM To: [hidden email] Subject: RE : Vendor Webinar Hi. The "sign up" link does not work, at least from France. I have several colleagues interrested in such a webminar. How can we sign up? Thanks Sandrine ________________________________________ De : Confocal Microscopy List [[hidden email]] de la part de Grace Chojnowski [[hidden email]] Date d'envoi : jeudi 28 octobre 2010 01:54 À : [hidden email] Objet : Re: Vendor Webinar Hi Ian, I am setting up the seminar room for the webinar for next week, is there going to be any interaction with the audience? Q and A s etc? Kind Regards, Grace Grace Chojnowski Flow Cytometry and Confocal Microscopy Laboratory Manager Queensland Institute of Medical Research Brisbane, QLD, AUSTRALIA [hidden email] +61 7 3362 0314. 6+61 414 956 752 7+61 7 3362 0107 http://www.qimr.edu.au/flow -----Original Message----- From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Clements, Ian Sent: Friday, 22 October 2010 8:28 AM To: [hidden email] Subject: Re: Vendor Webinar ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** +++++Commercial Posting+++++ Hello Confocal List Members I would like to invite you to attend our upcoming online seminar: Light Microscopy Fundamentals Presented by Paul Goodwin Technical Fellow & Director of Advanced Applications Applied Precision, Inc November 3, 2010 at the following times: 6 a.m., 11 a.m., and 6 p.m. PST The light microscope is one of the most important tools in biology. This webinar will cover image formation in the light microscope and discuss the essential elements of the light microscope - magnification, resolution, and contrast. We will also cover how aberrations impact contrast and resolution and discuss methods to assess optical performance. We will then discuss the relationship of sample preparation, the optical pathway and the microscope in its entirety. We will finish with practical recommendations for obtaining the best performance out of your microscope and the best data from your microscopy-based experiments. Sign up online at http://www.apiwebinars.webex.com Ian Clements Product Manager - DeltaVision OMX Systems This email message, together with any attachments, is for the sole use of the intended recipient(s) and is the confidential information of Applied Precision Inc. If you are not the intended recipient, your review, use, disclosure, copying or dissemination of this email message or its attachments, or the information contained therein, is strictly prohibited. If you are not the intended recipient or if you think this email was sent to you in error, please notify the sender by reply email and delete this message and its attachments, as well as all copies, from your system. This email message, together with any attachments, is for the sole use of the intended recipient(s) and is the confidential information of Applied Precision Inc. If you are not the intended recipient, your review, use, disclosure, copying or dissemination of this email message or its attachments, or the information contained therein, is strictly prohibited. If you are not the intended recipient or if you think this email was sent to you in error, please notify the sender by reply email and delete this message and its attachments, as well as all copies, from your system. |
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