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

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

gkowalsky6AtGmail
>
> 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]&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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Re: Odp: microscope name retrieval using only the image file

Fred Damen
Greetings,

To look at, search, and figure out nonhuman readable files I use 'gvim',
vi improved, vim.org.  Works on all platforms.  Gvim has a readonly mode,
gvim -R or view, that will not overwrite the file.  Once the image file is
opened, use Tools>Convert to HEX, which will show the file in standard
hexdump format allowing you to search for the string you are looking for.
For the hardcore you can also use this to edit these files (if you opened
them writable of course). Also check out File>Split Diff With...

Since I am on the subject of Gvim, I would like to make two requests: In
Compiler.java:
Please remove the line:
                        errors.setFont(new Font("Monospaced", Font.PLAIN, 12));
from void showErrors(String s).
The Editor window that the error messages are displayed in remembers what
font style and size that I told it to use before... but I have to use Make
bigger/Make smaller for it to display as such.

And, could there be an option to allow the compiler to send the error
messages to stderr, as it normally would when run from the command line.
I would like to use gvim as the edit/compile/run.  Gvim has a nice
quickfix functionality, albeit requires access to the compiler syntax
error messages on stderr.

Note to do "Compile and Run..." from Gvim and/or to .gvimrc or just
execute: :map <silent> <F9> :silent w<bar>!imagej -o -e 'run("Compile and
Run...","compile=%:p");'<CR>
(one line) and then use F9 instead of Ctrl-r.  It helps to run gvim from
the directory you want the File Browser to default to as ImageJ does not
seem to remember the last directory visited running the plugin in this
way.

Thanks in advance,

Fred

On Mon, April 6, 2020 11:14 am, gkowalsky6AtGmail wrote:
>>
>> 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/
...

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html