http://imagej.273.s1.nabble.com/File-formats-and-pixel-size-tp5024686p5024735.html
Edit > Options > ImageJ2, "Use SCIFIO when opening files (BETA!)". It is
> 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/>
>