ImageJ - Re: Odp: microscope name retrieval using only the image file

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Re: Odp: microscope name retrieval using only the image file

Posted by gkowalsky6AtGmail on Apr 06, 2020; 4:14pm
URL: http://imagej.273.s1.nabble.com/Re-Odp-microscope-name-retrieval-using-only-the-image-file-tp5023180.html

>
> As it was already said, which metadata is recorded is dependent on
integrator/installer/end-user configuration and software defaults. However,
my recollections from working with old and legacy integrated systems are
that some information was written into the headers or footers of the image
file itself. In these cases, I opened the image file in any simplest
ASCII/ANSI/Unicode text editor and just tried to find anything resembled
human language.

For this, any code editor capable of opening large files as simple text
would work. On Windows, right-click on file icon, select "Open with..." ->
"Choose default program..." etc. Make sure always to UNCHECK the "Always
use the selected program to open this kind of file", in order not to break
local file associations.

NOTE: for additional safety, open a copy or backup of file in question, not
the originals. In this case, one's not risking to corrupt the original data
file because of text editors' bugs or local workstation failure.

I do understand it could be a time consuming task...

Best of luck,
Grr

----
GK_at http://gikscientific.com/

Date: Sat, 4 Apr 2020 15:56:03 +0000

> From: "Cammer, Michael" <[hidden email]>
> Subject: Re: microscope name retrieval using only the image file
>
> 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]> 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
>

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