Olympus VSI Reader ActionBar
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Dear ImageJ / Fiji Users,
We've recently finished testing a piece of code to help read .VSI files taken with an Olympus slide scanner. Thanks to Jerome Mutterer's ActionBar plugin and the LOCI Bio-Formats plugin, we've been able to build a simple to use image cropper/importer for these large (>100k x 100k pixels) images. The concept is simple. Be able to navigate your data, crop and save regions, adjust calibration and help in the processing pipeline (Loading macros for each image as they are being exported). The ActionBar is available from our website http://biop/INFO_completed_projects.html The above page also contains a short PDF tutorial on the buttons and how to use them, as well as a sample dataset. We're still working on this plugin and will keep you updated of any changes, and in return we'd like to hear from you be it bugs, questions or just a friendly hello! Many thanks to the OME team for all the help they provided in getting BioFormats to work for us and this particular format! Best regards, Oli Olivier Burri Engineer, Development in Image Processing BioImaging and Optics platform (PTBIOP) Tel: [+4121 69] 39629 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Olympus VSI Reader ActionBar
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On Monday 23 Jul 2012 16:02:21 you wrote:
> Dear ImageJ / Fiji Users, > > We've recently finished testing a piece of code to help read .VSI files > taken with an Olympus slide scanner. > > Thanks to Jerome Mutterer's ActionBar plugin and the LOCI Bio-Formats > plugin, we've been able to build a simple to use image cropper/importer for > these large (>100k x 100k pixels) images. > > The concept is simple. Be able to navigate your data, crop and save regions, > adjust calibration and help in the processing pipeline (Loading macros for > each image as they are being exported). > > The ActionBar is available from our website > > http://biop/INFO_completed_projects.html Unfortunately that website (or biop.com) do not show up at all in Firefox or in Konqueror. Cheers Gabriel -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi Gabriel,
On Mon, 23 Jul 2012, Gabriel Landini wrote: > On Monday 23 Jul 2012 16:02:21 you wrote: > > > The ActionBar is available from our website > > > > http://biop/INFO_completed_projects.html > > Unfortunately that website (or biop.com) do not show up at all in > Firefox or in Konqueror. It is http://biop.epfl.ch/INFO_completed_projects.html Also note that contrary to what is said on the website, ActionBar is not included in the .zip, which is good, because that version might go stale very quickly. A much better idea would have been to offer this package as an update site. Ciao, Dscho -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Olympus VSI Reader ActionBar
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Hi Gabriel, Johannes,
> Also note that contrary to what is said on the website, ActionBar is not > included in the .zip, which is good, because that version might go stale > very quickly. Indeed the ActionBar plugin is not included with the download. We'll change the text on the website as soon as possible (i.e. tomorrow). Thank you for pointing it out. > A much better idea would have been to offer this package as an update > site. I apologize but I do not understand what you mean by "as an update site". If you can point me in the right direction, then I'll set it up. > It is http://biop.epfl.ch/INFO_completed_projects.html So sorry about this! Seeing as I use the internal link so often, I fail to notice when the ".epfl.ch" is missing! Thank you for pointing it out. Best, Oli Olivier Burri Engineer, Development in Image Processing BioImaging and Optics platform (PTBIOP) Tel: [+4121 69] 39629 ________________________________________ From: ImageJ Interest Group [[hidden email]] on behalf of Johannes Schindelin [[hidden email]] Sent: Monday, July 23, 2012 5:26 PM To: [hidden email] Subject: Re: Olympus VSI Reader ActionBar Hi Gabriel, On Mon, 23 Jul 2012, Gabriel Landini wrote: > On Monday 23 Jul 2012 16:02:21 you wrote: > > > The ActionBar is available from our website > > > > http://biop/INFO_completed_projects.html > > Unfortunately that website (or biop.com) do not show up at all in > Firefox or in Konqueror. It is http://biop.epfl.ch/INFO_completed_projects.html Also note that contrary to what is said on the website, ActionBar is not included in the .zip, which is good, because that version might go stale very quickly. A much better idea would have been to offer this package as an update site. Ciao, Dscho -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi Olivier,
On Mon, 23 Jul 2012, Burri Olivier wrote: > > A much better idea would have been to offer this package as an update > > site. > I apologize but I do not understand what you mean by "as an update > site". If you can point me in the right direction, then I'll set it up. http://fiji.sc/Adding_Update_Sites Ciao, Johannes -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Olympus VSI Reader ActionBar
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In reply to this post by Olivier Burri
Hi all,
Can someone explain how i can install this. Do i need to install jerome mutterer's ActionBar plugin first? And is the vsi reader a plugin also? So i know how to install it so it will appear in the fiji menu. Thanks, Matt On 23 Jul 2012, at 16:02, Burri Olivier wrote: > Dear ImageJ / Fiji Users, > > We've recently finished testing a piece of code to help read .VSI > files taken with an Olympus slide scanner. > > Thanks to Jerome Mutterer's ActionBar plugin and the LOCI Bio- > Formats plugin, we've been able to build a simple to use image > cropper/importer for these large (>100k x 100k pixels) images. > > The concept is simple. Be able to navigate your data, crop and save > regions, adjust calibration and help in the processing pipeline > (Loading macros for each image as they are being exported). > > The ActionBar is available from our website > > http://biop/INFO_completed_projects.html > > The above page also contains a short PDF tutorial on the buttons and > how to use them, as well as a sample dataset. > > We're still working on this plugin and will keep you updated of any > changes, and in return we'd like to hear from you be it bugs, > questions or just a friendly hello! > > Many thanks to the OME team for all the help they provided in > getting BioFormats to work for us and this particular format! > > Best regards, > > Oli > > Olivier Burri > Engineer, Development in Image Processing > BioImaging and Optics platform (PTBIOP) > Tel: [+4121 69] 39629 > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > Matt Pearson Microscopy and Imaging Facility MRC Human Genetics Unit University of Edinburgh Crewe Road Edinburgh EH4 2XU Tel: 0131 467 8425 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Olympus VSI Reader ActionBar
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Dear Matthew,
Step-by-step. 1. Install ActionBar.jar in your plugins folder http://imagejdocu.tudor.lu/doku.php?id=plugin:utilities:action_bar:start 2. Download the .zip file from http://biop.epfl.ch/INFO_completed_projects.html#vsi-reader<http://biop/INFO_completed_projects.html#vsi-reader> 3. Unzip its contents into the plugins folder At the end of the operation, your path to the actionbar should look like this PATH_TO_FIJI / Plugins / ActionBar / BIOP Bars After this, inside the "Biop Bars" folder there should be the "icons" folder as well as "BIOP_VSI_Reader.ijm" file The VSI reader is an ActionBar, meaning in our case a mix of macros and calls to plugins. It will appear under Plugins->ActionBar->BIOP Bars->BIOP VSI Reader Hope this helps! Best, Oli Olivier Burri Engineer, Development in Image Processing BioImaging and Optics platform (PTBIOP) Tel: [+4121 69] 39629 ________________________________ From: ImageJ Interest Group [[hidden email]] on behalf of Matthew Pearson [[hidden email]] Sent: Tuesday, July 24, 2012 3:18 PM To: [hidden email] Subject: Re: Olympus VSI Reader ActionBar Hi all, Can someone explain how i can install this. Do i need to install jerome mutterer's ActionBar plugin first? And is the vsi reader a plugin also? So i know how to install it so it will appear in the fiji menu. Thanks, Matt On 23 Jul 2012, at 16:02, Burri Olivier wrote: > Dear ImageJ / Fiji Users, > > We've recently finished testing a piece of code to help read .VSI > files taken with an Olympus slide scanner. > > Thanks to Jerome Mutterer's ActionBar plugin and the LOCI Bio- > Formats plugin, we've been able to build a simple to use image > cropper/importer for these large (>100k x 100k pixels) images. > > The concept is simple. Be able to navigate your data, crop and save > regions, adjust calibration and help in the processing pipeline > (Loading macros for each image as they are being exported). > > The ActionBar is available from our website > > http://biop/INFO_completed_projects.html > > The above page also contains a short PDF tutorial on the buttons and > how to use them, as well as a sample dataset. > > We're still working on this plugin and will keep you updated of any > changes, and in return we'd like to hear from you be it bugs, > questions or just a friendly hello! > > Many thanks to the OME team for all the help they provided in > getting BioFormats to work for us and this particular format! > > Best regards, > > Oli > > Olivier Burri > Engineer, Development in Image Processing > BioImaging and Optics platform (PTBIOP) > Tel: [+4121 69] 39629 > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- Matt Pearson Microscopy and Imaging Facility MRC Human Genetics Unit University of Edinburgh Crewe Road Edinburgh EH4 2XU Tel: 0131 467 8425 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Olympus VSI Reader ActionBar
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In reply to this post by PEARSON Matthew
Hi,
I got the action bar to work with the sample data set. However, when i wanted to read the documentation, the link took me to documentation for the massive stitcher, not the vsi reader. is this a web page error or has the documentation not been finished yet? Rob On 24/07/2012 14:18, Matthew Pearson wrote: > Hi all, > > Can someone explain how i can install this. Do i need to install > jerome mutterer's ActionBar plugin first? And is the vsi reader a > plugin also? So i know how to install it so it will appear in the > fiji menu. > > Thanks, > Matt > On 23 Jul 2012, at 16:02, Burri Olivier wrote: > >> Dear ImageJ / Fiji Users, >> >> We've recently finished testing a piece of code to help read .VSI >> files taken with an Olympus slide scanner. >> >> Thanks to Jerome Mutterer's ActionBar plugin and the LOCI Bio-Formats >> plugin, we've been able to build a simple to use image >> cropper/importer for these large (>100k x 100k pixels) images. >> >> The concept is simple. Be able to navigate your data, crop and save >> regions, adjust calibration and help in the processing pipeline >> (Loading macros for each image as they are being exported). >> >> The ActionBar is available from our website >> >> http://biop/INFO_completed_projects.html >> >> The above page also contains a short PDF tutorial on the buttons and >> how to use them, as well as a sample dataset. >> >> We're still working on this plugin and will keep you updated of any >> changes, and in return we'd like to hear from you be it bugs, >> questions or just a friendly hello! >> >> Many thanks to the OME team for all the help they provided in getting >> BioFormats to work for us and this particular format! >> >> Best regards, >> >> Oli >> >> Olivier Burri >> Engineer, Development in Image Processing >> BioImaging and Optics platform (PTBIOP) >> Tel: [+4121 69] 39629 >> >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> > > -- > Matt Pearson > Microscopy and Imaging Facility > MRC Human Genetics Unit > University of Edinburgh > Crewe Road > Edinburgh > EH4 2XU > > Tel: 0131 467 8425 > > > > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Olympus VSI Reader ActionBar
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Dear Rob,
This was indeed an error which was corrected this morning. Feel free to try again now. http://biop.epfl.ch/INFO_completed_projects.html#vsi-reader Sorry for the inconvenience and best regards, Oli Olivier Burri Engineer, Development in Image Processing BioImaging and Optics platform (PTBIOP) Tel: [+4121 69] 39629 ________________________________________ From: ImageJ Interest Group [[hidden email]] on behalf of Rob van 't Hof [[hidden email]] Sent: Tuesday, July 24, 2012 5:15 PM To: [hidden email] Subject: Re: Olympus VSI Reader ActionBar Hi, I got the action bar to work with the sample data set. However, when i wanted to read the documentation, the link took me to documentation for the massive stitcher, not the vsi reader. is this a web page error or has the documentation not been finished yet? Rob On 24/07/2012 14:18, Matthew Pearson wrote: > Hi all, > > Can someone explain how i can install this. Do i need to install > jerome mutterer's ActionBar plugin first? And is the vsi reader a > plugin also? So i know how to install it so it will appear in the > fiji menu. > > Thanks, > Matt > On 23 Jul 2012, at 16:02, Burri Olivier wrote: > >> Dear ImageJ / Fiji Users, >> >> We've recently finished testing a piece of code to help read .VSI >> files taken with an Olympus slide scanner. >> >> Thanks to Jerome Mutterer's ActionBar plugin and the LOCI Bio-Formats >> plugin, we've been able to build a simple to use image >> cropper/importer for these large (>100k x 100k pixels) images. >> >> The concept is simple. Be able to navigate your data, crop and save >> regions, adjust calibration and help in the processing pipeline >> (Loading macros for each image as they are being exported). >> >> The ActionBar is available from our website >> >> http://biop/INFO_completed_projects.html >> >> The above page also contains a short PDF tutorial on the buttons and >> how to use them, as well as a sample dataset. >> >> We're still working on this plugin and will keep you updated of any >> changes, and in return we'd like to hear from you be it bugs, >> questions or just a friendly hello! >> >> Many thanks to the OME team for all the help they provided in getting >> BioFormats to work for us and this particular format! >> >> Best regards, >> >> Oli >> >> Olivier Burri >> Engineer, Development in Image Processing >> BioImaging and Optics platform (PTBIOP) >> Tel: [+4121 69] 39629 >> >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> > > -- > Matt Pearson > Microscopy and Imaging Facility > MRC Human Genetics Unit > University of Edinburgh > Crewe Road > Edinburgh > EH4 2XU > > Tel: 0131 467 8425 > > > > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > -- > 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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