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File formats and pixel size

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AAM71

File formats and pixel size

Dear Listers,

I need some help from your collective knowledge and experience about file formats and ImageJ. Currently, I am using Velox software (Thermo Fisher Scientific) to operate Ceta CMOS camera on my Talos electron microscope. It is a great program with great and convenient user interface substituting the older clunky TIA software.

However, there is a small caveat - image formats. Original image format called "emd" is supposed to be a kind of hdf5, but I was not able to find any free image manipulation program that can easily read that.

So, the only choice I have is to convert emd file to tiff or mrc files (by included batch converter with Velox). And that is where my problem lies.

If I just drag and drop tiff/mrc files to ImageJ/Fiji then pixel size is not recognized. If you would open them using Bioformats then pixel size could be read properly. Also, if I save an image opened with Bioformats as tiff then pixel size is readable again.

Of course, I have written small script that can do this in batch mode for all my files. But it looks not very elegant and still does not answer the question why pixel size cannot be read by standard ImageJ/Fiji.

You can try it yourself with example files that are here: https://drive.google.com/drive/folders/13rKcUHrgHwFxZZoLsiXjlW2IxwjFeZ8p?usp=sharing

In that folder you will find:
Test.emd - original Velox file
Test.mrc and Test.tif - file converted by Velox
Test.tif_to_IJ.tif - file was opened with Bioformats and saved with ImageJ tiff option

I had some discussions with Velox team and their explanation is the following:

"We dive into details, apparently it looks like ImageJ is still reading pixel size information from dpi field. It is not something we can use: if you use these fields, then copy/paste into other programs becoming crazy. For example, if you paste such image in the word, it often tries to put image in the document by using physical dimensions pixels/dpi. As a result, people were getting 50x50nm image in the document, which was not possible to see after print".

So, my question is - is it possible to change the way how ImageJ is reading pixel size?

I have a bit more in depth explanations from Velox team about their formats:

quote begins========================================================

I think there are two places to pay attention to:

1.New standard we are using is xml in the custom field of tiff file and it contains all possible metadata, not just pixel size. So, this is the most extensive information, and I would recommend to use it if there is interest to access not just pixel size

Tiff metadata format

When exporting tiff raw data (16 bit tiff eport), the metadata is added to the tiff fields:
- All metadata is placed in a custom private tiff tag in xml format:
- Private Tiff tag 34683 is used to store the XML data
- FeiMetadata1.0-updated.xsd describes the format (ftp://ftp.vsg3d.com/private/MASTERS/Velox/Velox/FeiMetadata1.0-updated.xsd).

2. However, in the past we also used txt tags, which are still used in SDB and many of our SW packages still did not switch to the new format. It was enabled in Velox 3.0. It might be more useful for multiple package compatibility. Pixel size is placed in a custom private tiff tag in xt format if pixel size is in meter:

a) Private Tiff tag 34682 is used to store the text:

Beam: Beam, Scan
Scan: PixelWidth, PixelHeight
EScan: PixelWidth, PixelHeight

Example

[Beam]
Beam=EBeam
Scan=EScan

[Scan]
PixelWidth=2.69792e-009
PixelHeight=2.69792e-009

[EScan]
PixelWidth=2.69792e-009
PixelHeight=2.69792e-009

quote ends===========================================

Best regards,
Alex

--
Dr. Aleksandr Mironov MD, PhD
Senior Experimental Officer
D.1527, M.Smith Building
EM Core Facility (FBMH)
RRID: SCR_021147
University of Manchester
Oxford Road
Manchester
M13 9PT
UK

Tel. +44-(0)161-275-5645
E-mail: [hidden email]
Visit our Intranet EMCF web-page<https://app.bmh.manchester.ac.uk/facilities/research/electronmicroscopy/default.aspx>
Visit our EMCF Microsoft Team<https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77>
Visit our external EMCF web-page<https://www.bmh.manchester.ac.uk/research/facilities/electron-microscopy/>
<https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77>

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

Herbie

Re: File formats and pixel size

Greetings Aleksandr,

I'm far from sure where you see inconveniences.

If I understand correctly, you will be happy if ImageJ were able to open
the file "Test.mrc".

If you install BioFormats as a plugin in ImageJ, you will be able to
open this file in ImageJ.
(At least I could open it in ImageJ and it is shown as image having the
size 4.30 x 4.30 microns.)

Now my question:
Why do you think that this approach is perhaps not suited or inconvenient?

Regards

Herbie

:::::::::::::::::::::::::::::::::::::::::::::::
Am 03.06.21 um 17:06 schrieb Aleksandr Mironov:

> Dear Listers,
>
> I need some help from your collective knowledge and experience about file formats and ImageJ. Currently, I am using Velox software (Thermo Fisher Scientific) to operate Ceta CMOS camera on my Talos electron microscope. It is a great program with great and convenient user interface substituting the older clunky TIA software.
>
> However, there is a small caveat - image formats. Original image format called "emd" is supposed to be a kind of hdf5, but I was not able to find any free image manipulation program that can easily read that.
>
> So, the only choice I have is to convert emd file to tiff or mrc files (by included batch converter with Velox). And that is where my problem lies.
>
> If I just drag and drop tiff/mrc files to ImageJ/Fiji then pixel size is not recognized. If you would open them using Bioformats then pixel size could be read properly. Also, if I save an image opened with Bioformats as tiff then pixel size is readable again.
>
> Of course, I have written small script that can do this in batch mode for all my files. But it looks not very elegant and still does not answer the question why pixel size cannot be read by standard ImageJ/Fiji.
>
> You can try it yourself with example files that are here: https://drive.google.com/drive/folders/13rKcUHrgHwFxZZoLsiXjlW2IxwjFeZ8p?usp=sharing
>
> In that folder you will find:
> Test.emd - original Velox file
> Test.mrc and Test.tif - file converted by Velox
> Test.tif_to_IJ.tif - file was opened with Bioformats and saved with ImageJ tiff option
>
> I had some discussions with Velox team and their explanation is the following:
>
> "We dive into details, apparently it looks like ImageJ is still reading pixel size information from dpi field. It is not something we can use: if you use these fields, then copy/paste into other programs becoming crazy. For example, if you paste such image in the word, it often tries to put image in the document by using physical dimensions pixels/dpi. As a result, people were getting 50x50nm image in the document, which was not possible to see after print".
>
> So, my question is - is it possible to change the way how ImageJ is reading pixel size?
>
>
> I have a bit more in depth explanations from Velox team about their formats:
>
> quote begins========================================================
>
> I think there are two places to pay attention to:
>
> 1.New standard we are using is xml in the custom field of tiff file and it contains all possible metadata, not just pixel size. So, this is the most extensive information, and I would recommend to use it if there is interest to access not just pixel size
>
> Tiff metadata format
>
> When exporting tiff raw data (16 bit tiff eport), the metadata is added to the tiff fields:
> - All metadata is placed in a custom private tiff tag in xml format:
> - Private Tiff tag 34683 is used to store the XML data
> - FeiMetadata1.0-updated.xsd describes the format (ftp://ftp.vsg3d.com/private/MASTERS/Velox/Velox/FeiMetadata1.0-updated.xsd).
>
> 2. However, in the past we also used txt tags, which are still used in SDB and many of our SW packages still did not switch to the new format. It was enabled in Velox 3.0. It might be more useful for multiple package compatibility. Pixel size is placed in a custom private tiff tag in xt format if pixel size is in meter:
>
> a) Private Tiff tag 34682 is used to store the text:
>
> Beam: Beam, Scan
> Scan: PixelWidth, PixelHeight
> EScan: PixelWidth, PixelHeight
>
> Example
>
> [Beam]
> Beam=EBeam
> Scan=EScan
>
> [Scan]
> PixelWidth=2.69792e-009
> PixelHeight=2.69792e-009
>
> [EScan]
> PixelWidth=2.69792e-009
> PixelHeight=2.69792e-009
>
> quote ends===========================================
>
> Best regards,
> Alex
>
> --
> Dr. Aleksandr Mironov MD, PhD
> Senior Experimental Officer
> D.1527, M.Smith Building
> EM Core Facility (FBMH)
> RRID: SCR_021147
> University of Manchester
> Oxford Road
> Manchester
> M13 9PT
> UK
>
> Tel. +44-(0)161-275-5645
> E-mail: [hidden email]
> Visit our Intranet EMCF web-page<https://app.bmh.manchester.ac.uk/facilities/research/electronmicroscopy/default.aspx>
> Visit our EMCF Microsoft Team<https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77>
> Visit our external EMCF web-page<https://www.bmh.manchester.ac.uk/research/facilities/electron-microscopy/>
> <https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

AAM71

Re: File formats and pixel size

Dear Herbie,

ImageJ/Fiji are able to open both tiff and mrc file by using Bioformats plugin (Sorry, if I was unclear). But this method asks for several clicks through menu and involves search for the source folder (in file explorer). If you work with one file - it is fine. However, if you working on many files, then it mounts to a significant degree.

I would prefer open the folder/folders with necessary files and drag/drop them directly into ImageJ/Fiji. But this mode results in wrong pixel size.
When you deal with a lot of users many of whom are quite inexperienced in image manipulation/processing then this will result in a lot of frustration.

Best regards,
Alex

--
Dr. Aleksandr Mironov MD, PhD
Senior Experimental Officer
D.1527, M.Smith Building
EM Core Facility (FBMH)
RRID: SCR_021147
University of Manchester
Oxford Road
Manchester
M13 9PT
UK

Tel. +44-(0)161-275-5645
E-mail: [hidden email]
Visit our Intranet EMCF web-page<https://app.bmh.manchester.ac.uk/facilities/research/electronmicroscopy/default.aspx>
Visit our EMCF Microsoft Team<https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77>
Visit our external EMCF web-page<https://www.bmh.manchester.ac.uk/research/facilities/electron-microscopy/>
<https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77>

________________________________
From: Herbie <[hidden email]>
Sent: 03 June 2021 16:48
To: [hidden email] <[hidden email]>
Subject: Re: File formats and pixel size

Greetings Aleksandr,

I'm far from sure where you see inconveniences.

If I understand correctly, you will be happy if ImageJ were able to open
the file "Test.mrc".

If you install BioFormats as a plugin in ImageJ, you will be able to
open this file in ImageJ.
(At least I could open it in ImageJ and it is shown as image having the
size 4.30 x 4.30 microns.)

Now my question:
Why do you think that this approach is perhaps not suited or inconvenient?

Regards

Herbie

:::::::::::::::::::::::::::::::::::::::::::::::
Am 03.06.21 um 17:06 schrieb Aleksandr Mironov:

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

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

Herbie

Re: File formats and pixel size

Aleksandr,

if you are fluent in Java, then write an importer for ImageJ that
handles the desired file types. If not, why do you think a tiny macro
that handles the "clicks" for you is clumsy? You can distribute it to
your colleagues and everything is fine.

There are hundreds of special image file types around and the most
important ones can be opened by using BioFormats. ImageJ is not a image
file converter and as such can't be blamed for not being able to open
special file types.

I think using a macro is the way to go. It can be made to open all files
in a directory, if this is desired.

Good luck

Herbie

:::::::::::::::::::::::::::::::::::::::::::::::
Am 03.06.21 um 18:19 schrieb Aleksandr Mironov:

> Dear Herbie,
>
> ImageJ/Fiji are able to open both tiff and mrc file by using Bioformats plugin (Sorry, if I was unclear). But this method asks for several clicks through menu and involves search for the source folder (in file explorer). If you work with one file - it is fine. However, if you working on many files, then it mounts to a significant degree.
>
> I would prefer open the folder/folders with necessary files and drag/drop them directly into ImageJ/Fiji. But this mode results in wrong pixel size.
> When you deal with a lot of users many of whom are quite inexperienced in image manipulation/processing then this will result in a lot of frustration.
>
> Best regards,
> Alex
>
>
> --
> Dr. Aleksandr Mironov MD, PhD
> Senior Experimental Officer
> D.1527, M.Smith Building
> EM Core Facility (FBMH)
> RRID: SCR_021147
> University of Manchester
> Oxford Road
> Manchester
> M13 9PT
> UK
>
> Tel. +44-(0)161-275-5645
> E-mail: [hidden email]
> Visit our Intranet EMCF web-page<https://app.bmh.manchester.ac.uk/facilities/research/electronmicroscopy/default.aspx>
> Visit our EMCF Microsoft Team<https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77>
> Visit our external EMCF web-page<https://www.bmh.manchester.ac.uk/research/facilities/electron-microscopy/>
> <https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77>
>
> ________________________________
> From: Herbie <[hidden email]>
> Sent: 03 June 2021 16:48
> To: [hidden email] <[hidden email]>
> Subject: Re: File formats and pixel size
>
> Greetings Aleksandr,
>
> I'm far from sure where you see inconveniences.
>
> If I understand correctly, you will be happy if ImageJ were able to open
> the file "Test.mrc".
>
> If you install BioFormats as a plugin in ImageJ, you will be able to
> open this file in ImageJ.
> (At least I could open it in ImageJ and it is shown as image having the
> size 4.30 x 4.30 microns.)
>
> Now my question:
> Why do you think that this approach is perhaps not suited or inconvenient?
>
> Regards
>
> Herbie
>
> :::::::::::::::::::::::::::::::::::::::::::::::
> Am 03.06.21 um 17:06 schrieb Aleksandr Mironov:
>> Dear Listers,
>>
>> I need some help from your collective knowledge and experience about file formats and ImageJ. Currently, I am using Velox software (Thermo Fisher Scientific) to operate Ceta CMOS camera on my Talos electron microscope. It is a great program with great and convenient user interface substituting the older clunky TIA software.
>>
>> However, there is a small caveat - image formats. Original image format called "emd" is supposed to be a kind of hdf5, but I was not able to find any free image manipulation program that can easily read that.
>>
>> So, the only choice I have is to convert emd file to tiff or mrc files (by included batch converter with Velox). And that is where my problem lies.
>>
>> If I just drag and drop tiff/mrc files to ImageJ/Fiji then pixel size is not recognized. If you would open them using Bioformats then pixel size could be read properly. Also, if I save an image opened with Bioformats as tiff then pixel size is readable again.
>>
>> Of course, I have written small script that can do this in batch mode for all my files. But it looks not very elegant and still does not answer the question why pixel size cannot be read by standard ImageJ/Fiji.
>>
>> You can try it yourself with example files that are here: https://drive.google.com/drive/folders/13rKcUHrgHwFxZZoLsiXjlW2IxwjFeZ8p?usp=sharing
>>
>> In that folder you will find:
>> Test.emd - original Velox file
>> Test.mrc and Test.tif - file converted by Velox
>> Test.tif_to_IJ.tif - file was opened with Bioformats and saved with ImageJ tiff option
>>
>> I had some discussions with Velox team and their explanation is the following:
>>
>> "We dive into details, apparently it looks like ImageJ is still reading pixel size information from dpi field. It is not something we can use: if you use these fields, then copy/paste into other programs becoming crazy. For example, if you paste such image in the word, it often tries to put image in the document by using physical dimensions pixels/dpi. As a result, people were getting 50x50nm image in the document, which was not possible to see after print".
>>
>> So, my question is - is it possible to change the way how ImageJ is reading pixel size?
>>
>>
>> I have a bit more in depth explanations from Velox team about their formats:
>>
>> quote begins========================================================
>>
>> I think there are two places to pay attention to:
>>
>> 1.New standard we are using is xml in the custom field of tiff file and it contains all possible metadata, not just pixel size. So, this is the most extensive information, and I would recommend to use it if there is interest to access not just pixel size
>>
>> Tiff metadata format
>>
>> When exporting tiff raw data (16 bit tiff eport), the metadata is added to the tiff fields:
>> - All metadata is placed in a custom private tiff tag in xml format:
>> - Private Tiff tag 34683 is used to store the XML data
>> - FeiMetadata1.0-updated.xsd describes the format (ftp://ftp.vsg3d.com/private/MASTERS/Velox/Velox/FeiMetadata1.0-updated.xsd).
>>
>> 2. However, in the past we also used txt tags, which are still used in SDB and many of our SW packages still did not switch to the new format. It was enabled in Velox 3.0. It might be more useful for multiple package compatibility. Pixel size is placed in a custom private tiff tag in xt format if pixel size is in meter:
>>
>> a) Private Tiff tag 34682 is used to store the text:
>>
>> Beam: Beam, Scan
>> Scan: PixelWidth, PixelHeight
>> EScan: PixelWidth, PixelHeight
>>
>> Example
>>
>> [Beam]
>> Beam=EBeam
>> Scan=EScan
>>
>> [Scan]
>> PixelWidth=2.69792e-009
>> PixelHeight=2.69792e-009
>>
>> [EScan]
>> PixelWidth=2.69792e-009
>> PixelHeight=2.69792e-009
>>
>> quote ends===========================================
>>
>> Best regards,
>> Alex
>>
>> --
>> Dr. Aleksandr Mironov MD, PhD
>> Senior Experimental Officer
>> D.1527, M.Smith Building
>> EM Core Facility (FBMH)
>> RRID: SCR_021147
>> University of Manchester
>> Oxford Road
>> Manchester
>> M13 9PT
>> UK
>>
>> Tel. +44-(0)161-275-5645
>> E-mail: [hidden email]
>> Visit our Intranet EMCF web-page<https://app.bmh.manchester.ac.uk/facilities/research/electronmicroscopy/default.aspx>
>> Visit our EMCF Microsoft Team<https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77>
>> Visit our external EMCF web-page<https://www.bmh.manchester.ac.uk/research/facilities/electron-microscopy/>
>> <https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

AAM71

Re: File formats and pixel size

Herbie,

I appreciate your comment but it is not very helpful. I am not fluent in Java and I have described my problem (related to users). Tiff and are not "special" file formats - they are quite common and adhere to recognized and published specifications.

I will ask it in different way:

1) Is it true that ImageJ reads pixel size from dpi field, meaning that it has quite clumsy compatibility with other scientific programs?

2) Are there any way to make Bioformats plugin as default way of opening files (even when they are dragged and dropped)?

Regards,
Alex

<https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77>

________________________________
From: Herbie <[hidden email]>
Sent: 03 June 2021 17:35
To: [hidden email] <[hidden email]>
Subject: Re: File formats and pixel size

Aleksandr,

if you are fluent in Java, then write an importer for ImageJ that
handles the desired file types. If not, why do you think a tiny macro
that handles the "clicks" for you is clumsy? You can distribute it to
your colleagues and everything is fine.

There are hundreds of special image file types around and the most
important ones can be opened by using BioFormats. ImageJ is not a image
file converter and as such can't be blamed for not being able to open
special file types.

I think using a macro is the way to go. It can be made to open all files
in a directory, if this is desired.

Good luck

Herbie

:::::::::::::::::::::::::::::::::::::::::::::::
Am 03.06.21 um 18:19 schrieb Aleksandr Mironov:

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

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

Herbie

Re: File formats and pixel size

Sorry Aleksandr,

for not being very helpful.

I can't comment on #1 because I don't have enough time to explore the
code but you could, because ImageJ is open source.

re 2:
Fiji should allow this.
It opens your image "Test.mrc" per drag&drop but the scale isn't set.
Don't ask me why. I'm not familiar enough with Fiji and its inclusion of
BioFormats.

"Tiff and are not "special" file formats"

No doubt but I was writing about the ".emd"- and ".mrc"-formats because
these are the formats that you get from your device-software and I
understand that these are the formats that you like to open directly
from ImageJ.

I just had a look at the data of your image "Test.tif" by using the
ImageJ plugin "TIFF_Dumper". It appears as if the proper metadata is
present, pixel spacing included:
...
[Scan]
PixelWidth=1.049762e-09
PixelHeight=1.049762e-09
[EScan]
PixelWidth=1.049762e-09
PixelHeight=1.049762e-09
...
<PixelSize>
<X unit="m">1.0497621669736808e-09</X>
<Y unit="m">1.0497621669736808e-09</Y>
</PixelSize>
...

I doubt however that if it is possible to access this information by
using macro code. Consequently, you'd need a plugin that in turn
requires Java-skills.

Again not very helpful but I doubt that you'll find a ready-made
solution for your special requirements.

Regards

Herbie

:::::::::::::::::::::::::::::::::::::::::::::::
Am 03.06.21 um 18:49 schrieb Aleksandr Mironov:

> Herbie,
>
> I appreciate your comment but it is not very helpful. I am not fluent in Java and I have described my problem (related to users). Tiff and are not "special" file formats - they are quite common and adhere to recognized and published specifications.
>
> I will ask it in different way:
>
> 1) Is it true that ImageJ reads pixel size from dpi field, meaning that it has quite clumsy compatibility with other scientific programs?
>
> 2) Are there any way to make Bioformats plugin as default way of opening files (even when they are dragged and dropped)?
>
> Regards,
> Alex
>
> <https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77>
>
> ________________________________
> From: Herbie <[hidden email]>
> Sent: 03 June 2021 17:35
> To: [hidden email] <[hidden email]>
> Subject: Re: File formats and pixel size
>
> Aleksandr,
>
> if you are fluent in Java, then write an importer for ImageJ that
> handles the desired file types. If not, why do you think a tiny macro
> that handles the "clicks" for you is clumsy? You can distribute it to
> your colleagues and everything is fine.
>
> There are hundreds of special image file types around and the most
> important ones can be opened by using BioFormats. ImageJ is not a image
> file converter and as such can't be blamed for not being able to open
> special file types.
>
> I think using a macro is the way to go. It can be made to open all files
> in a directory, if this is desired.
>
> Good luck
>
> Herbie
>
> :::::::::::::::::::::::::::::::::::::::::::::::
> Am 03.06.21 um 18:19 schrieb Aleksandr Mironov:
>> Dear Herbie,
>>
>> ImageJ/Fiji are able to open both tiff and mrc file by using Bioformats plugin (Sorry, if I was unclear). But this method asks for several clicks through menu and involves search for the source folder (in file explorer). If you work with one file - it is fine. However, if you working on many files, then it mounts to a significant degree.
>>
>> I would prefer open the folder/folders with necessary files and drag/drop them directly into ImageJ/Fiji. But this mode results in wrong pixel size.
>> When you deal with a lot of users many of whom are quite inexperienced in image manipulation/processing then this will result in a lot of frustration.
>>
>> Best regards,
>> Alex
>>
>>
>> --
>> Dr. Aleksandr Mironov MD, PhD
>> Senior Experimental Officer
>> D.1527, M.Smith Building
>> EM Core Facility (FBMH)
>> RRID: SCR_021147
>> University of Manchester
>> Oxford Road
>> Manchester
>> M13 9PT
>> UK
>>
>> Tel. +44-(0)161-275-5645
>> E-mail: [hidden email]
>> Visit our Intranet EMCF web-page<https://app.bmh.manchester.ac.uk/facilities/research/electronmicroscopy/default.aspx>
>> Visit our EMCF Microsoft Team<https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77>
>> Visit our external EMCF web-page<https://www.bmh.manchester.ac.uk/research/facilities/electron-microscopy/>
>> <https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77><https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77>
>>
>> ________________________________
>> From: Herbie <[hidden email]>
>> Sent: 03 June 2021 16:48
>> To: [hidden email] <[hidden email]>
>> Subject: Re: File formats and pixel size
>>
>> Greetings Aleksandr,
>>
>> I'm far from sure where you see inconveniences.
>>
>> If I understand correctly, you will be happy if ImageJ were able to open
>> the file "Test.mrc".
>>
>> If you install BioFormats as a plugin in ImageJ, you will be able to
>> open this file in ImageJ.
>> (At least I could open it in ImageJ and it is shown as image having the
>> size 4.30 x 4.30 microns.)
>>
>> Now my question:
>> Why do you think that this approach is perhaps not suited or inconvenient?
>>
>> Regards
>>
>> Herbie
>>
>> :::::::::::::::::::::::::::::::::::::::::::::::
>> Am 03.06.21 um 17:06 schrieb Aleksandr Mironov:
>>> Dear Listers,
>>>
>>> I need some help from your collective knowledge and experience about file formats and ImageJ. Currently, I am using Velox software (Thermo Fisher Scientific) to operate Ceta CMOS camera on my Talos electron microscope. It is a great program with great and convenient user interface substituting the older clunky TIA software.
>>>
>>> However, there is a small caveat - image formats. Original image format called "emd" is supposed to be a kind of hdf5, but I was not able to find any free image manipulation program that can easily read that.
>>>
>>> So, the only choice I have is to convert emd file to tiff or mrc files (by included batch converter with Velox). And that is where my problem lies.
>>>
>>> If I just drag and drop tiff/mrc files to ImageJ/Fiji then pixel size is not recognized. If you would open them using Bioformats then pixel size could be read properly. Also, if I save an image opened with Bioformats as tiff then pixel size is readable again.
>>>
>>> Of course, I have written small script that can do this in batch mode for all my files. But it looks not very elegant and still does not answer the question why pixel size cannot be read by standard ImageJ/Fiji.
>>>
>>> You can try it yourself with example files that are here: https://drive.google.com/drive/folders/13rKcUHrgHwFxZZoLsiXjlW2IxwjFeZ8p?usp=sharing
>>>
>>> In that folder you will find:
>>> Test.emd - original Velox file
>>> Test.mrc and Test.tif - file converted by Velox
>>> Test.tif_to_IJ.tif - file was opened with Bioformats and saved with ImageJ tiff option
>>>
>>> I had some discussions with Velox team and their explanation is the following:
>>>
>>> "We dive into details, apparently it looks like ImageJ is still reading pixel size information from dpi field. It is not something we can use: if you use these fields, then copy/paste into other programs becoming crazy. For example, if you paste such image in the word, it often tries to put image in the document by using physical dimensions pixels/dpi. As a result, people were getting 50x50nm image in the document, which was not possible to see after print".
>>>
>>> So, my question is - is it possible to change the way how ImageJ is reading pixel size?
>>>
>>>
>>> I have a bit more in depth explanations from Velox team about their formats:
>>>
>>> quote begins========================================================
>>>
>>> I think there are two places to pay attention to:
>>>
>>> 1.New standard we are using is xml in the custom field of tiff file and it contains all possible metadata, not just pixel size. So, this is the most extensive information, and I would recommend to use it if there is interest to access not just pixel size
>>>
>>> Tiff metadata format
>>>
>>> When exporting tiff raw data (16 bit tiff eport), the metadata is added to the tiff fields:
>>> - All metadata is placed in a custom private tiff tag in xml format:
>>> - Private Tiff tag 34683 is used to store the XML data
>>> - FeiMetadata1.0-updated.xsd describes the format (ftp://ftp.vsg3d.com/private/MASTERS/Velox/Velox/FeiMetadata1.0-updated.xsd).
>>>
>>> 2. However, in the past we also used txt tags, which are still used in SDB and many of our SW packages still did not switch to the new format. It was enabled in Velox 3.0. It might be more useful for multiple package compatibility. Pixel size is placed in a custom private tiff tag in xt format if pixel size is in meter:
>>>
>>> a) Private Tiff tag 34682 is used to store the text:
>>>
>>> Beam: Beam, Scan
>>> Scan: PixelWidth, PixelHeight
>>> EScan: PixelWidth, PixelHeight
>>>
>>> Example
>>>
>>> [Beam]
>>> Beam=EBeam
>>> Scan=EScan
>>>
>>> [Scan]
>>> PixelWidth=2.69792e-009
>>> PixelHeight=2.69792e-009
>>>
>>> [EScan]
>>> PixelWidth=2.69792e-009
>>> PixelHeight=2.69792e-009
>>>
>>> quote ends===========================================
>>>
>>> Best regards,
>>> Alex
>>>
>>> --
>>> Dr. Aleksandr Mironov MD, PhD
>>> Senior Experimental Officer
>>> D.1527, M.Smith Building
>>> EM Core Facility (FBMH)
>>> RRID: SCR_021147
>>> University of Manchester
>>> Oxford Road
>>> Manchester
>>> M13 9PT
>>> UK
>>>
>>> Tel. +44-(0)161-275-5645
>>> E-mail: [hidden email]
>>> Visit our Intranet EMCF web-page<https://app.bmh.manchester.ac.uk/facilities/research/electronmicroscopy/default.aspx>
>>> Visit our EMCF Microsoft Team<https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77>
>>> Visit our external EMCF web-page<https://www.bmh.manchester.ac.uk/research/facilities/electron-microscopy/>
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>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>
>>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
>
> --
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>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Herbie

Re: File formats and pixel size

In reply to this post by AAM71

Good evening Alex,

further inspection reveals that ImageJ stores the TIFF scale information
as spatial resolution, i.e. as the inverse of the pixel spacing. The
TIFF-tags are:
X_RESOLUTION
Y_RESOLUTION

Your image file "Test.tif" contains the spatial resolutions as:
65450 = 9525967/1
65451 = 9525967/1

Maybe this helps with further discussions.

Regards

Herbie

:::::::::::::::::::::::::::::::::::::::::::::::
Am 03.06.21 um 18:49 schrieb Aleksandr Mironov:

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Gabriel Landini

Re: File formats and pixel size

In reply to this post by AAM71

Hello Aleksandr,

On Thursday, 3 June 2021 17:49:21 BST Aleksandr Mironov wrote:
> I will ask it in different way:
> 1) Is it true that ImageJ reads pixel size from dpi field, meaning that it
> has quite clumsy compatibility with other scientific programs?

I do not think so. IJ seems to store the values in the right place. There is no "dpi field", but these 'baseline' tags:

Tiff tags 282 (TIFFTAG_XRESOLUTION), 283 (TIFFTAG_YRESOLUTION) and 296 (TIFFTAG_RESOLUTIONUNIT)

The pertinent bit, I think, in TiffEncoder.java is:

if (fi.unit!=null && fi.pixelWidth!=0 && fi.pixelHeight!=0) {
writeEntry(out, TiffDecoder.X_RESOLUTION, 5, 1, tagDataOffset);
writeEntry(out, TiffDecoder.Y_RESOLUTION, 5, 1, tagDataOffset+8);
tagDataOffset += SCALE_DATA_SIZE;
int unit = 1;
if (fi.unit.equals("inch"))
unit = 2;
else if (fi.unit.equals("cm"))
unit = 3;
writeEntry(out, TiffDecoder.RESOLUTION_UNIT, 3, 1, unit);
}

Note that the TIFF reference says: "It is not mandatory that the image be actually displayed or printed at the size implied by this parameter. It is up to the application to use this information as it wishes." The 50nm image anecdote is most likely due to Word wrongly assuming that 'image resolution' implies the printer 'output size'.

But the important point is that storing metadata in a private tag does not make it automagically "a standard" so all other programs *know* what to do with it. Private tags are a "standard way" for software authors to extend the format and store and retrieve whatever they want to put in there. Baseline tags should be interpreted correctly by all other programs, but it would be naive to expect the same for private tags because there is no way to know in advance what another software might have put in there. The tiff reader has to implement the recognition of the new tag and what it contains (and do something with that contents).

That being said, it possible to write a file reader that overrides the baseline tags if the private Tiff tag 34683 exists and use its data instead. As far as I understand it, the company implemented it about 6 yrs ago? (according to this OME bug report https://trac.openmicroscopy.org/ome/ticket/12743 ) so no surprise it has not been implemented widely if this was the first time that the issue has been raised.

I see that Herbie has just replied about this, too.

Cheers

Gabriel

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Wayne Rasband-2

Re: File formats and pixel size

In reply to this post by AAM71

> On Jun 3, 2021, at 12:19 PM, Aleksandr Mironov <[hidden email]> wrote:
>
> Dear Herbie,
>
> ImageJ/Fiji are able to open both tiff and mrc file by using Bioformats plugin (Sorry, if I was unclear). But this method asks for several clicks through menu and involves search for the source folder (in file explorer). If you work with one file - it is fine. However, if you working on many files, then it mounts to a significant degree.
>
> I would prefer open the folder/folders with necessary files and drag/drop them directly into ImageJ/Fiji. But this mode results in wrong pixel size.

Bio-Formats will open images dragged and dropped on the ImageJ window when you enable “Use SCIFIO when opening files (BETA)” in Fiji's Edit>Options>Image2 dialog but there appears to be a bug that causes the image size of your test image to be set to 0.00x0.00 pixels. What does work is opening the Plugins>Bio-Formats>Bio-Formats Plugins Shortcuts Window and dragging and dropping files on it.

-wayne

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Cardone, Giovanni

Re: File formats and pixel size

Dear Aleksandr,

as Wayne suggested, you could use the ImageJ2 option to use the scifio library as default.
When used with mrc files, the pixel size is properly read and reported, but unfortunately the physical unit reported is wrong. By default mrc files store in their header, although indirectly, the pixel size in angstroms, and the bioformats library converts the value to microns. However, this does not happen with the mentioned option, and in your case ImageJ reports the pixel size as 10.4976 pixels, instead of Angstroms. You could try and highlight this issue to the Fiji developers.
By the way, the issue with the mrc files arises from the fact that there is a default reader (Open_MRC_Leginon.class) that is invoked when a mrc file is dragged and dropped. The reader is very basic, and ignores most of the content of the header in the files, including any extension from the most recent 2014 mrc format specifications, which instead the Velox software implements (but probably also the bioformats ignore it).
I hope this helps.

Giovanni

-----Original Message-----
From: ImageJ Interest Group <[hidden email]> On Behalf Of Wayne Rasband
Sent: Friday, June 4, 2021 5:42 AM
To: [hidden email]
Subject: Re: File formats and pixel size

> On Jun 3, 2021, at 12:19 PM, Aleksandr Mironov <[hidden email]> wrote:
>
> Dear Herbie,
>
> ImageJ/Fiji are able to open both tiff and mrc file by using Bioformats plugin (Sorry, if I was unclear). But this method asks for several clicks through menu and involves search for the source folder (in file explorer). If you work with one file - it is fine. However, if you working on many files, then it mounts to a significant degree.
>
> I would prefer open the folder/folders with necessary files and drag/drop them directly into ImageJ/Fiji. But this mode results in wrong pixel size.

Bio-Formats will open images dragged and dropped on the ImageJ window when you enable “Use SCIFIO when opening files (BETA)” in Fiji's Edit>Options>Image2 dialog but there appears to be a bug that causes the image size of your test image to be set to 0.00x0.00 pixels. What does work is opening the Plugins>Bio-Formats>Bio-Formats Plugins Shortcuts Window and dragging and dropping files on it.

-wayne

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gnelson

Re: File formats and pixel size

In reply to this post by AAM71

Hi Aleksandr,

I wasn't aware there was a default mrc file reader as Giovanni points out, as I don't work with those. However, if you have installed bioformats correctly, dragging a bioformats readable file onto the imagej toolbar will invoke the Bioformats plugin to open the file, meaning you don't have to navigate through a file system (apart from the fact you had to do that to get to the file to drag it in the first place!). At least, this is how it operates on the versions of ImageJ and Fiji I have installed on linux, mac and windows systems. You will still be asked how you would like bioformats to open the file however. A simple batch script to convert all to tifs is the way round this. If your scalings are all constant, you can even concatenate them all together so you only have to drag one tif after conversion! So perhaps your question is one of how to write a batch file or use the batch process option in Imagej?

Glyn

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AAM71

Re: File formats and pixel size

In reply to this post by Wayne Rasband-2

Thank you, Wayne! That is very useful trick! If there is a bug in Fiji that you mentioned, should I report it to Fiji team?

I thank Herbie, Giovanni and Gabriel for very useful insights into the internal working of ImageJ/Fiji!

I appreciate your help very much.

best regards,
Alex
________________________________
From: Wayne Rasband <[hidden email]>
Sent: 04 June 2021 04:42
To: [hidden email] <[hidden email]>
Subject: Re: File formats and pixel size

> On Jun 3, 2021, at 12:19 PM, Aleksandr Mironov <[hidden email]> wrote:
>
> Dear Herbie,
>
> ImageJ/Fiji are able to open both tiff and mrc file by using Bioformats plugin (Sorry, if I was unclear). But this method asks for several clicks through menu and involves search for the source folder (in file explorer). If you work with one file - it is fine. However, if you working on many files, then it mounts to a significant degree.
>
> I would prefer open the folder/folders with necessary files and drag/drop them directly into ImageJ/Fiji. But this mode results in wrong pixel size.

Bio-Formats will open images dragged and dropped on the ImageJ window when you enable “Use SCIFIO when opening files (BETA)” in Fiji's Edit>Options>Image2 dialog but there appears to be a bug that causes the image size of your test image to be set to 0.00x0.00 pixels. What does work is opening the Plugins>Bio-Formats>Bio-Formats Plugins Shortcuts Window and dragging and dropping files on it.

-wayne

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Herbie

Re: File formats and pixel size

In reply to this post by AAM71

Sent on behalf of Philippe CARL @ Université de Strasbourg
__________________________

Dear Aleksandr,
Similarly to you I don't like to use the Bioformats importer not only
due to its displayed selection window but also and especially the needed
(incredibly huge) time just for opening a simple pictures stack.
As such "heavy duty" workflow may be acceptable in the case you just
need to open a couple of such files, it becomes way to heavy when you
need to work with a lot of such files.
Thus what I did was to follow exactly the recommandation of Herbie of
writing a macro that allows to perform an ad hoc formatting of files
"wrongly read by ImageJ" through a Drag&Drop opening.
And I added this reformatting code within the StartupMacros.txt and call
it through a Shortcut.
So if you wish I could make this code available for you to have a
starting point in order to create your own solution.
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
__________________________

Am 03.06.21 um 17:06 schrieb Aleksandr Mironov:

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AAM71

Re: File formats and pixel size

Dear Philippe,

I already have working macro converting tiff/mrc that I call using windows batch file. I was just hoping that I am missing something in standard drag/drop file opening.
However, I will still appreciate your code as it may teach me couple of things.

Best regards,
Alex

________________________________
From: Herbie <[hidden email]>
Sent: 04 June 2021 14:41
To: [hidden email] <[hidden email]>
Subject: Re: File formats and pixel size

Sent on behalf of Philippe CARL @ Université de Strasbourg
__________________________

Dear Aleksandr,
Similarly to you I don't like to use the Bioformats importer not only
due to its displayed selection window but also and especially the needed
(incredibly huge) time just for opening a simple pictures stack.
As such "heavy duty" workflow may be acceptable in the case you just
need to open a couple of such files, it becomes way to heavy when you
need to work with a lot of such files.
Thus what I did was to follow exactly the recommandation of Herbie of
writing a macro that allows to perform an ad hoc formatting of files
"wrongly read by ImageJ" through a Drag&Drop opening.
And I added this reformatting code within the StartupMacros.txt and call
it through a Shortcut.
So if you wish I could make this code available for you to have a
starting point in order to create your own solution.
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
__________________________

Am 03.06.21 um 17:06 schrieb Aleksandr Mironov:

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CARL Philippe (LBP)

Re: File formats and pixel size

Dear Aleksandr,
You will find the advertised file under the following link:
http://punias.free.fr/ImageJ/StartupMacros.txt
As you will see this code will be doing a little bit more than what you requested.
It had been written in order to open iMIC data (a microscope that was manufactured by the company Till Photonics) and thus will add an iMIC icon to the ImageJ window for which you could define different opening options by making a mouse right click on the icon.
And the file reformatting (following a "regular ImageJ Drag&Drop opening") is done either through a mouse left click on the icon of just using the F8 key.
So please enjoy and feel free to contact me in the case you have further questions.
My best regards,
Philippe

----- Mail original -----
De: "Aleksandr Mironov" <[hidden email]>
À: "imagej" <[hidden email]>, "CARL Philippe, LBP" <[hidden email]>
Envoyé: Vendredi 4 Juin 2021 15:49:34
Objet: Re: File formats and pixel size

Dear Philippe,

I already have working macro converting tiff/mrc that I call using windows batch file. I was just hoping that I am missing something in standard drag/drop file opening.
However, I will still appreciate your code as it may teach me couple of things.

Best regards,
Alex

From: Herbie <[hidden email]>
Sent: 04 June 2021 14:41
To: [hidden email] <[hidden email]>
Subject: Re: File formats and pixel size
Sent on behalf of Philippe CARL @ Université de Strasbourg
__________________________

Dear Aleksandr,
Similarly to you I don't like to use the Bioformats importer not only
due to its displayed selection window but also and especially the needed
(incredibly huge) time just for opening a simple pictures stack.
As such "heavy duty" workflow may be acceptable in the case you just
need to open a couple of such files, it becomes way to heavy when you
need to work with a lot of such files.
Thus what I did was to follow exactly the recommandation of Herbie of
writing a macro that allows to perform an ad hoc formatting of files
"wrongly read by ImageJ" through a Drag&Drop opening.
And I added this reformatting code within the StartupMacros.txt and call
it through a Shortcut.
So if you wish I could make this code available for you to have a
starting point in order to create your own solution.
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

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Herbie

ImageJ Icon / Logo etc.

In reply to this post by AAM71

Dear listers,

just curious, did the icon/logo of ImageJ change recently and if so, why?
See attached screen-shot of <https://forum.image.sc/tag/imagej>

Furthermore, ImageJ is now listed as image.sc-"Community Partner" (see
attached screen-shot of forum.image.sc) which, according to the rules
<https://forum.image.sc/t/about-the-community-partners-category/33685>,
means that the Forum is to be used as the "primary recommended
discussion channel".

Does this mean that our beloved IJ-list must be shut down?

Somehow clueless

Herbie
::::::::::::::::

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Latest imagej topics - Image sc Forum.png (103K) Download Attachment

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Curtis Rueden-2

Re: File formats and pixel size

In reply to this post by AAM71

Hi Alex,

> Are there any way to make Bioformats plugin as default way of
> opening files (even when they are dragged and dropped)?

If you use ImageJ2 (for example, if you use Fiji), there is an option in
Edit > Options > ImageJ2, "Use SCIFIO when opening files (BETA!)". It is
off by default for compatibility reasons, but when checked, it makes
drag-and-drop prefer SCIFIO and Bio-Formats over ImageJ 1.x's file I/O
routines.

Regards,
Curtis

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Curtis Rueden
Software architect, LOCI/Eliceiri lab - https://uw-loci.github.io/
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Have you tried the Image.sc Forum? https://forum.image.sc/

On Thu, Jun 3, 2021 at 11:49 AM Aleksandr Mironov <
[hidden email]> wrote:

> Herbie,
>
> I appreciate your comment but it is not very helpful. I am not fluent in
> Java and I have described my problem (related to users). Tiff and are not
> "special" file formats - they are quite common and adhere to recognized and
> published specifications.
>
> I will ask it in different way:
>
> 1) Is it true that ImageJ reads pixel size from dpi field, meaning that it
> has quite clumsy compatibility with other scientific programs?
>
> 2) Are there any way to make Bioformats plugin as default way of opening
> files (even when they are dragged and dropped)?
>
> Regards,
> Alex
>
> ________________________________
> From: Herbie <[hidden email]>
> Sent: 03 June 2021 17:35
> To: [hidden email] <[hidden email]>
> Subject: Re: File formats and pixel size
>
> Aleksandr,
>
> if you are fluent in Java, then write an importer for ImageJ that
> handles the desired file types. If not, why do you think a tiny macro
> that handles the "clicks" for you is clumsy? You can distribute it to
> your colleagues and everything is fine.
>
> There are hundreds of special image file types around and the most
> important ones can be opened by using BioFormats. ImageJ is not a image
> file converter and as such can't be blamed for not being able to open
> special file types.
>
> I think using a macro is the way to go. It can be made to open all files
> in a directory, if this is desired.
>
> Good luck
>
> Herbie
>
> :::::::::::::::::::::::::::::::::::::::::::::::
> Am 03.06.21 um 18:19 schrieb Aleksandr Mironov:
> > Dear Herbie,
> >
> > ImageJ/Fiji are able to open both tiff and mrc file by using Bioformats
> plugin (Sorry, if I was unclear). But this method asks for several clicks
> through menu and involves search for the source folder (in file explorer).
> If you work with one file - it is fine. However, if you working on many
> files, then it mounts to a significant degree.
> >
> > I would prefer open the folder/folders with necessary files and
> drag/drop them directly into ImageJ/Fiji. But this mode results in wrong
> pixel size.
> > When you deal with a lot of users many of whom are quite inexperienced
> in image manipulation/processing then this will result in a lot of
> frustration.
> >
> > Best regards,
> > Alex
> >
> >
> > --
> > Dr. Aleksandr Mironov MD, PhD
> > Senior Experimental Officer
> > D.1527, M.Smith Building
> > EM Core Facility (FBMH)
> > RRID: SCR_021147
> > University of Manchester
> > Oxford Road
> > Manchester
> > M13 9PT
> > UK
> >
> > Tel. +44-(0)161-275-5645
> > E-mail: [hidden email]
> > Visit our Intranet EMCF web-page<
> https://app.bmh.manchester.ac.uk/facilities/research/electronmicroscopy/default.aspx
> >
> > Visit our EMCF Microsoft Team<
> https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77
> >
> > Visit our external EMCF web-page<
> https://www.bmh.manchester.ac.uk/research/facilities/electron-microscopy/>
> >
> > ________________________________
> > From: Herbie <[hidden email]>
> > Sent: 03 June 2021 16:48
> > To: [hidden email] <[hidden email]>
> > Subject: Re: File formats and pixel size
> >
> > Greetings Aleksandr,
> >
> > I'm far from sure where you see inconveniences.
> >
> > If I understand correctly, you will be happy if ImageJ were able to open
> > the file "Test.mrc".
> >
> > If you install BioFormats as a plugin in ImageJ, you will be able to
> > open this file in ImageJ.
> > (At least I could open it in ImageJ and it is shown as image having the
> > size 4.30 x 4.30 microns.)
> >
> > Now my question:
> > Why do you think that this approach is perhaps not suited or
> inconvenient?
> >
> > Regards
> >
> > Herbie
> >
> > :::::::::::::::::::::::::::::::::::::::::::::::
> > Am 03.06.21 um 17:06 schrieb Aleksandr Mironov:
> >> Dear Listers,
> >>
> >> I need some help from your collective knowledge and experience about
> file formats and ImageJ. Currently, I am using Velox software (Thermo
> Fisher Scientific) to operate Ceta CMOS camera on my Talos electron
> microscope. It is a great program with great and convenient user interface
> substituting the older clunky TIA software.
> >>
> >> However, there is a small caveat - image formats. Original image format
> called "emd" is supposed to be a kind of hdf5, but I was not able to find
> any free image manipulation program that can easily read that.
> >>
> >> So, the only choice I have is to convert emd file to tiff or mrc files
> (by included batch converter with Velox). And that is where my problem lies.
> >>
> >> If I just drag and drop tiff/mrc files to ImageJ/Fiji then pixel size
> is not recognized. If you would open them using Bioformats then pixel size
> could be read properly. Also, if I save an image opened with Bioformats as
> tiff then pixel size is readable again.
> >>
> >> Of course, I have written small script that can do this in batch mode
> for all my files. But it looks not very elegant and still does not answer
> the question why pixel size cannot be read by standard ImageJ/Fiji.
> >>
> >> You can try it yourself with example files that are here:
> https://drive.google.com/drive/folders/13rKcUHrgHwFxZZoLsiXjlW2IxwjFeZ8p?usp=sharing
> >>
> >> In that folder you will find:
> >> Test.emd - original Velox file
> >> Test.mrc and Test.tif - file converted by Velox
> >> Test.tif_to_IJ.tif - file was opened with Bioformats and saved with
> ImageJ tiff option
> >>
> >> I had some discussions with Velox team and their explanation is the
> following:
> >>
> >> "We dive into details, apparently it looks like ImageJ is still reading
> pixel size information from dpi field. It is not something we can use: if
> you use these fields, then copy/paste into other programs becoming crazy.
> For example, if you paste such image in the word, it often tries to put
> image in the document by using physical dimensions pixels/dpi. As a
> result, people were getting 50x50nm image in the document, which was not
> possible to see after print".
> >>
> >> So, my question is - is it possible to change the way how ImageJ is
> reading pixel size?
> >>
> >>
> >> I have a bit more in depth explanations from Velox team about their
> formats:
> >>
> >> quote begins========================================================
> >>
> >> I think there are two places to pay attention to:
> >>
> >> 1.New standard we are using is xml in the custom field of tiff file and
> it contains all possible metadata, not just pixel size. So, this is the
> most extensive information, and I would recommend to use it if there is
> interest to access not just pixel size
> >>
> >> Tiff metadata format
> >>
> >> When exporting tiff raw data (16 bit tiff eport), the metadata is added
> to the tiff fields:
> >> - All metadata is placed in a custom private tiff tag in xml format:
> >> - Private Tiff tag 34683 is used to store the XML data
> >> - FeiMetadata1.0-updated.xsd describes the format (
> ftp://ftp.vsg3d.com/private/MASTERS/Velox/Velox/FeiMetadata1.0-updated.xsd
> ).
> >>
> >> 2. However, in the past we also used txt tags, which are still
> used in SDB and many of our SW packages still did not switch to the new
> format. It was enabled in Velox 3.0. It might be more useful for multiple
> package compatibility. Pixel size is placed in a custom private tiff tag in
> xt format if pixel size is in meter:
> >>
> >> a) Private Tiff tag 34682 is used to store the text:
> >>
> >> Beam: Beam, Scan
> >> Scan: PixelWidth, PixelHeight
> >> EScan: PixelWidth, PixelHeight
> >>
> >> Example
> >>
> >> [Beam]
> >> Beam=EBeam
> >> Scan=EScan
> >>
> >> [Scan]
> >> PixelWidth=2.69792e-009
> >> PixelHeight=2.69792e-009
> >>
> >> [EScan]
> >> PixelWidth=2.69792e-009
> >> PixelHeight=2.69792e-009
> >>
> >> quote ends===========================================
> >>
> >> Best regards,
> >> Alex
> >>
> >> --
> >> Dr. Aleksandr Mironov MD, PhD
> >> Senior Experimental Officer
> >> D.1527, M.Smith Building
> >> EM Core Facility (FBMH)
> >> RRID: SCR_021147
> >> University of Manchester
> >> Oxford Road
> >> Manchester
> >> M13 9PT
> >> UK
> >>
> >> Tel. +44-(0)161-275-5645
> >> E-mail: [hidden email]
> >> Visit our Intranet EMCF web-page<
> https://app.bmh.manchester.ac.uk/facilities/research/electronmicroscopy/default.aspx
> >
> >> Visit our EMCF Microsoft Team<
> https://teams.microsoft.com/l/team/19%3acbd90045098142469739abf26c6a94b4%40thread.tacv2/conversations?groupId=158933c5-fb09-4039-8f12-69b0b0426882&tenantId=c152cb07-614e-4abb-818a-f035cfa91a77
> >
> >> Visit our external EMCF web-page<
> https://www.bmh.manchester.ac.uk/research/facilities/electron-microscopy/>
>

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