Re: File formats and pixel size

Posted by Herbie on Jun 03, 2021; 5:20pm
URL: http://imagej.273.s1.nabble.com/File-formats-and-pixel-size-tp5024686p5024691.html

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. [phone]
>> 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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>>
>> ________________________________
>> 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. [phone]
>>> 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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>>>
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>>
>>
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>
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