olympus oir

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wm
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olympus oir

wm
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Is anyone who knows how to convert olympus format ".oir" to ".tif" or some other format that can be open in ImageJ? The old formats ".oib" and ".oif" can be easily converted with bioformat impoter.
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Re: olympus oir

Dotan
This post has NOT been accepted by the mailing list yet.
Historic as it is...
Olympus has an OlympusImageJPlugin ( http://imagej.net/OlympusImageJPlugin ) that supports the OIR (and VSI) format.
The plugin opens the file as a hyperstack with the correct calibration, LUT etc. but is limited by the file size and has some limitations with regard to scripting.
AFAIK there is no alternative open plugin (e.g. Bio-Formats).
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Re: olympus oir

cudmore
I am having trouble opening Olympus oir files using the Olympus provided
'OlympusViewer-Ver2.2.1' Fiji/ImageJ plugin. The plugin is available at:

   https://imagej.net/OlympusImageJPlugin


Any ideas on how to fix this?


OS versions:

 - Windows 7, macOS Sierra, macOS Mojave


Fiji/ImageJ versions:

 - Most recent download (both stock download and download after selecting
update).
 - Lifeline (2017)


Installing the 'OlympusViewer-Ver2.2.1' plugin:

 Copy the downloaded 'OlympusViewer-Ver2.2.1' folder into Fiji 'plugins'
folder
 

Running the plugin

 Select the Fiji/ImageJ menu 'Plugins - Olympus Viewer - Viewer'


The symptoms:

 - Selecting the menu 'Plugins - Olympus Viewer - Viewer' will run once and
produce an imageJ/Fiji stack with the images in the selected oir file.
 - After the first run, selecting the same menu does nothing, even after
   - Restarting Fiji
   - Reinstalling the plugins by replacing the plugins folder
'OlympusViewer-Ver2.2.1'
   - Reinstalling Fiji
   - Restarting the machine
   - I have not tried re-installing Java but suspect that might work?
   - On opening Fiji, each time the plugin menu 'Olympus Viewer - Viewer' is
selected, Fiji/ImageJ can not be 'quit' with the file menu but needs to be
force(d) quit.

In a cross post, I am also having problems opening Olympus oir files using
Fiji/ImageJ bio-formats and have posted the problems here:

https://forum.image.sc/t/problems-opening-olympus-oir-files-using-bio-formats/24747


p.s. shout out to Christophe Leterrier



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Re: olympus oir

Cammer, Michael-2
BioFormats importer works great.


Michael Cammer, Sr Research Scientist, DART Microscopy Laboratory

NYU Langone Health, 540 First Avenue, SK2 Microscopy Suite, New York, NY  10016

[hidden email]<mailto:[hidden email]>  http://nyulmc.org/micros  http://microscopynotes.com/

Voice direct only, no text or messages:  1-914-309-3270 and 1-646-501-0567



________________________________
From: cudmore <[hidden email]>
Sent: Wednesday, April 17, 2019 12:55:59 AM
To: [hidden email]
Subject: Re: olympus oir

I am having trouble opening Olympus oir files using the Olympus provided
'OlympusViewer-Ver2.2.1' Fiji/ImageJ plugin. The plugin is available at:

   https://urldefense.proofpoint.com/v2/url?u=https-3A__imagej.net_OlympusImageJPlugin&d=DwICAg&c=j5oPpO0eBH1iio48DtsedeElZfc04rx3ExJHeIIZuCs&r=hUBj2D5n6oKThx2L01qn8IORZb5f-ruLVXPmQ1zQNnM&m=0RNp16xYGEmbYFLXbyDhUz8L1hWGd9d1G2DnSvMvQEM&s=ku5EVPxolLPL0y-lMxW0gy5Vxc-hZ8OQdW8nIlvzEtk&e=


Any ideas on how to fix this?


OS versions:

 - Windows 7, macOS Sierra, macOS Mojave


Fiji/ImageJ versions:

 - Most recent download (both stock download and download after selecting
update).
 - Lifeline (2017)


Installing the 'OlympusViewer-Ver2.2.1' plugin:

 Copy the downloaded 'OlympusViewer-Ver2.2.1' folder into Fiji 'plugins'
folder


Running the plugin

 Select the Fiji/ImageJ menu 'Plugins - Olympus Viewer - Viewer'


The symptoms:

 - Selecting the menu 'Plugins - Olympus Viewer - Viewer' will run once and
produce an imageJ/Fiji stack with the images in the selected oir file.
 - After the first run, selecting the same menu does nothing, even after
   - Restarting Fiji
   - Reinstalling the plugins by replacing the plugins folder
'OlympusViewer-Ver2.2.1'
   - Reinstalling Fiji
   - Restarting the machine
   - I have not tried re-installing Java but suspect that might work?
   - On opening Fiji, each time the plugin menu 'Olympus Viewer - Viewer' is
selected, Fiji/ImageJ can not be 'quit' with the file menu but needs to be
force(d) quit.

In a cross post, I am also having problems opening Olympus oir files using
Fiji/ImageJ bio-formats and have posted the problems here:

https://urldefense.proofpoint.com/v2/url?u=https-3A__forum.image.sc_t_problems-2Dopening-2Dolympus-2Doir-2Dfiles-2Dusing-2Dbio-2Dformats_24747&d=DwICAg&c=j5oPpO0eBH1iio48DtsedeElZfc04rx3ExJHeIIZuCs&r=hUBj2D5n6oKThx2L01qn8IORZb5f-ruLVXPmQ1zQNnM&m=0RNp16xYGEmbYFLXbyDhUz8L1hWGd9d1G2DnSvMvQEM&s=oe4ZPgEj-bT6Oj_j5C-BNpD68O22hJW71wuq6TXNGtM&e=


p.s. shout out to Christophe Leterrier



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Sent from: https://urldefense.proofpoint.com/v2/url?u=http-3A__imagej.1557.x6.nabble.com_&d=DwICAg&c=j5oPpO0eBH1iio48DtsedeElZfc04rx3ExJHeIIZuCs&r=hUBj2D5n6oKThx2L01qn8IORZb5f-ruLVXPmQ1zQNnM&m=0RNp16xYGEmbYFLXbyDhUz8L1hWGd9d1G2DnSvMvQEM&s=ktrLHyHcxwShpgKO6zqaZacfxqmOlNdyHWRyEcfl5CY&e=

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ImageJ mailing list: https://urldefense.proofpoint.com/v2/url?u=http-3A__imagej.nih.gov_ij_list.html&d=DwICAg&c=j5oPpO0eBH1iio48DtsedeElZfc04rx3ExJHeIIZuCs&r=hUBj2D5n6oKThx2L01qn8IORZb5f-ruLVXPmQ1zQNnM&m=0RNp16xYGEmbYFLXbyDhUz8L1hWGd9d1G2DnSvMvQEM&s=W12NXdlTZCTAsdmxI1S6yySBlbdOgiLqhMgnDTaAmYs&e=

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