microscope name retrieval using only the image file
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microscope name retrieval using only the image file
 
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Hi
I would like to find out the name of the microscope which was used to take specific biological images. I have opened up "image info" while using the bio-formats importer which gave me more information on image parameters than without, but still no microscope name. I was wondering if any body knows how to retrieve this information with just the image file to hand? Many thanks Jessica -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: microscope name retrieval using only the image file
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Dear Jessica,
My answer to your request depends whether you want to answer your question on a single shot or regular basis ? For two microscopes I often use, I have written readers interpreting completely the meta data I'm interested in by using either the getMetadata("Info") or File.openAsString(path) methods and decomposing the obtained strings using the split(string, delimiters) method. But in the case I just need to get such an answer for a single file, I simply use (I'm under Windows) Total Commander (https://www.ghisler.com) which has a quite powerful file viewer (F3 key) which (by pressing the number keys) allows you to visualize your file in different formats. I choose then one that applies the best and browse through the data to get the information I'm looking for. Have a nice week-end. My best regards, Philippe Philippe CARL Laboratoire de Bioimagerie et Pathologies UMR 7021 CNRS - Université de Strasbourg Faculté de Pharmacie 74 route du Rhin 67401 ILLKIRCH Tel : +33(0)3 68 85 42 89 ----- Le 3 Avr 20, à 20:06, Jessica Chadwick [hidden email] a écrit : Hi I would like to find out the name of the microscope which was used to take specific biological images. I have opened up "image info" while using the bio-formats importer which gave me more information on image parameters than without, but still no microscope name. I was wondering if any body knows how to retrieve this information with just the image file to hand? Many thanks Jessica -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: microscope name retrieval using only the image file
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In reply to this post by Jessica Chadwick
Seems it depends on how the metadata are programmed by the microscope company and the settings for filers etc have to be programmed correctly by whoever sets up the scope. For instance, in the LIF file I checked from our SP8, which used to be a SP5, there is not name of the microscope anywhere, although maybe there is a number that might be meaningful if we know how to decode it.
A few examples I found using BioFormats 6.2.1. From Zeiss 880: Information|Instrument|Microscope|System #1 LSM 880, AxioObserver Information|Instrument|Objective|Immersion #1 Oil Information|Instrument|Objective|LensNA #1 1.4000000000000001 Information|Instrument|Objective|Manufacturer|Model #1 Plan-Apochromat 63x/1.4 Oil DIC M27 From Leica SP8 (note the stand is listed, but not the confocal model by name): Image|ATLConfocalSettingDefinition|ActiveCS_SubModeForRLDName Empty Image|ATLConfocalSettingDefinition|ActiveCS_SubModeForTLDName Scan-BF Image|ATLConfocalSettingDefinition|MicroscopeModel DM6B-Z-CS Image|ATLConfocalSettingDefinition|ObjectiveName HC PL APO CS2 63x/1.40 OIL Nikon A1 confocal: Camera Name Nikon A1plus Camera Settings #1 Camera Settings #2 CameraFamilyName Nikon A1 CameraUniqueName Nikon_A1_New CameraUserName Nikon A1plus m_CompanyString NIKON Instruments Inc. m_CopyrightString Copyright © 1991-2017 Laboratory Imaging, http://www.lim.cz m_GrabberString Nikon A1plus Confocal m_SWNameString NIS-Elements AR m_VersionString 5.02.00 (Build 1266) Patch 02 m_sXYFullName0 Ti2 XYDrive m_sXYKey0 XY Drive m_sXYPhysFullName0 Nikon Ti2 m_sXYShortName0 XY Drive m_sZFullName0 Ti2 ZDrive m_sZFullName1 Nikon A1 Piezo Z Drive m_sZKey0 Z Drive m_sZKey1 A1 Piezo Z m_sZPhysFullName0 Nikon Ti2 m_sZPhysFullName1 Nikon A1 Confocal m_sZShortName0 Z Drive m_sZShortName1 A1 Piezo Z m_sZoomFullName Ti2 Zoom m_sZoomPhysFullName Nikon Ti2 sObjective Plan Apo λ 60x Oil wsCameraName Nikon_A1_New wsObjectiveName Plan Apo λ 60x Oil (and a lot more references like these) Nikon Ti: Microscope Ti Microscope Microscope Settings Modality Widefield Fluorescence wsObjectiveName Plan Apo 20x DIC M N2 Camera Name Andor Zyla VSC-02048 Camera Settings Camera Type #1 Andor Zyla Camera Type #2 Andor Zyla CameraFamilyName Neo CameraName VSC-02048 m_CompanyString NIKON Corporation m_CopyrightString Copyright © 1991-2014 Laboratory Imaging, http://www.lim.cz m_GrabberString ANDOR Neo/Zyla m_SWNameString NIS-Elements AR m_VersionString 4.30.02 (Build 1053) 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: Ja <[hidden email]> Sent: Saturday, April 4, 2020 10:58:36 AM To: [hidden email] Subject: Odp: microscope name retrieval using only the image file [EXTERNAL] Give me a sample image, I will check if any meta about it is there. Dnia 3 kwietnia 2020 22:07 Jessica Chadwick <[hidden email]> napisał(a): Hi I would like to find out the name of the microscope which was used to take specific biological images. I have opened up "image info" while using the bio-formats importer which gave me more information on image parameters than without, but still no microscope name.� I was wondering if any body knows how to retrieve this information with just the image file to hand? Many thanks� Jessica -- ImageJ mailing list: imagej.nih.gov imagej.nih.gov -- ImageJ mailing list: https://urldefense.proofpoint.com/v2/url?u=http-3A__imagej.nih.gov_ij_list.html&d=DwIFaQ&c=j5oPpO0eBH1iio48DtsedeElZfc04rx3ExJHeIIZuCs&r=hUBj2D5n6oKThx2L01qn8IORZb5f-ruLVXPmQ1zQNnM&m=Un94NW-JDFc74vzwjbiF7zsITgAYWIEv3c1SbN7C05k&s=EZEu0nRU2W6RMW5LMvDYT7Elqm8msWJgSPsMv9slxaM&e= -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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