microscope name retrieval using only the image file

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microscope name retrieval using only the image file

Jessica Chadwick
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

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Re: microscope name retrieval using only the image file

CARL Philippe (LBP)
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

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Re: microscope name retrieval using only the image file

Cammer, Michael-3
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 &lt;[hidden email]&gt; 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 &#34;image
 info&#34; 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

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 ImageJ mailing list:  imagej.nih.gov imagej.nih.gov

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