ImageJ

Opening files from TIA software

_‹ Previous Topic Next Topic _›

Classic

List

Threaded

8 messages Options

Søren Roesgaard Nielsen

Opening files from TIA software

Hi

I am trying to open TEM files acuired using TIA software.

The file is a .emi file.

I have tried to install the following plugin:
http://imagej.nih.gov/ij/plugins/tia-reader.html

But I cannot get it to show up I Fiji, I gives the following error when I try to install it:
WARNING: The PluginClassLoader cannot be reset

Any suggestions?

Søren Roesgaard Nielsen
Ph.D. Student
Tel.: +45 28 78 14 25
Office: 1590-151
Email: [hidden email]<mailto:[hidden email]>

iNANO
Aarhus University
Gustav Wieds Vej 14
DK-8000 Aarhus
Web: www.inano.au.dk<https://mail.au.dk/owa/UrlBlockedError.aspx>

[http://t2.gstatic.com/images?q=tbn:ANd9GcSuNO--QyrO9DDzk905MnRZxHFnNvip2292d5KqdHoryiDJgcsH]

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

image002.jpg (9K) Download Attachment

Kenton Arkill

Re: Opening files from TIA software

I don't know about the error. However the pluggin in the plugging folder
appears in the in-out sub folder in the plugins tree. It also opens the
.ser files not the .emi files. Personally I then have a macro that converts
a folder of .ser into tif. No information (headers etc) are lost.
Not the answer but might help...
Kenton
On Jan 10, 2015 11:29 AM, "Søren Roesgaard Nielsen" <[hidden email]>
wrote:

> Hi
>
> I am trying to open TEM files acuired using TIA software.
>
> The file is a .emi file.
>
> I have tried to install the following plugin:
> http://imagej.nih.gov/ij/plugins/tia-reader.html
>
> But I cannot get it to show up I Fiji, I gives the following error when I
> try to install it:
> WARNING: The PluginClassLoader cannot be reset
>
> Any suggestions?
>
> Søren Roesgaard Nielsen
> Ph.D. Student
> Tel.: +45 28 78 14 25
> Office: 1590-151
> Email: [hidden email]<mailto:[hidden email]>
>
> iNANO
> Aarhus University
> Gustav Wieds Vej 14
> DK-8000 Aarhus
> Web: www.inano.au.dk<https://mail.au.dk/owa/UrlBlockedError.aspx>
>
> [
> http://t2.gstatic.com/images?q=tbn:ANd9GcSuNO--QyrO9DDzk905MnRZxHFnNvip2292d5KqdHoryiDJgcsH
> ]
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

Michael Elbaum

Re: Opening files from TIA software

I'm also using the plugin for .ser files, and re my earlier post about opening multiple files it is in fact macro-compatible. (Thanks to Aryeh Weiss and Nadav Elad.) It should be possible to have it open drag-and-drop according to instructions in a comment in the java source file, by modifying the HandleExtraFileTypes plugin. I didn't manage to make that work, but it raises the question that maybe there's some other plugin catching the .ser filetype on your system? Have you succeeded in adding other plugins or do you get the same error?

Kenton, any chance you could share the conversion macro? It would be very helpful to many of us using TIA!

Michael

________________________________________
From: ImageJ Interest Group [[hidden email]] on behalf of Kenton Arkill [[hidden email]]
Sent: Saturday, January 10, 2015 06:50
To: [hidden email]
Subject: Re: Opening files from TIA software

I don't know about the error. However the pluggin in the plugging folder
appears in the in-out sub folder in the plugins tree. It also opens the
.ser files not the .emi files. Personally I then have a macro that converts
a folder of .ser into tif. No information (headers etc) are lost.
Not the answer but might help...
Kenton
On Jan 10, 2015 11:29 AM, "Søren Roesgaard Nielsen" <[hidden email]>
wrote:

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

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

Kenton Arkill

Re: Opening files from TIA software

Here is the marco I use.
I normally have 2 files for each XX.emi and XX_1.ser. This macro gestured
of the _1.ser but a different version of the software might not have the _1
bit so will need altering. I've as yet not found a reason to keep the .emi
file afterwards. If you open the .tif as a text I think (I haven't checked)
that at the end is a list of microscope parameters which would have been in
the .emi, I've only used it when the scale became uncalibrated and had to
covert from the scope mag to actual scale....

Kenton

On 11 January 2015 at 04:01, Michael Elbaum <[hidden email]>
wrote:

> I'm also using the plugin for .ser files, and re my earlier post about
> opening multiple files it is in fact macro-compatible. (Thanks to Aryeh
> Weiss and Nadav Elad.) It should be possible to have it open drag-and-drop
> according to instructions in a comment in the java source file, by
> modifying the HandleExtraFileTypes plugin. I didn't manage to make that
> work, but it raises the question that maybe there's some other plugin
> catching the .ser filetype on your system? Have you succeeded in adding
> other plugins or do you get the same error?
>
> Kenton, any chance you could share the conversion macro? It would be very
> helpful to many of us using TIA!
>
> Michael
>
> ________________________________________
> From: ImageJ Interest Group [[hidden email]] on behalf of Kenton
> Arkill [[hidden email]]
> Sent: Saturday, January 10, 2015 06:50
> To: [hidden email]
> Subject: Re: Opening files from TIA software
>
> I don't know about the error. However the pluggin in the plugging folder
> appears in the in-out sub folder in the plugins tree. It also opens the
> .ser files not the .emi files. Personally I then have a macro that converts
> a folder of .ser into tif. No information (headers etc) are lost.
> Not the answer but might help...
> Kenton
> On Jan 10, 2015 11:29 AM, "Søren Roesgaard Nielsen" <[hidden email]
> >
> wrote:
>
> > Hi
> >
> > I am trying to open TEM files acuired using TIA software.
> >
> > The file is a .emi file.
> >
> > I have tried to install the following plugin:
> > http://imagej.nih.gov/ij/plugins/tia-reader.html
> >
> > But I cannot get it to show up I Fiji, I gives the following error when I
> > try to install it:
> > WARNING: The PluginClassLoader cannot be reset
> >
> > Any suggestions?
> >
> > Søren Roesgaard Nielsen
> > Ph.D. Student
> > Tel.: +45 28 78 14 25
> > Office: 1590-151
> > Email: [hidden email]<mailto:[hidden email]>
> >
> > iNANO
> > Aarhus University
> > Gustav Wieds Vej 14
> > DK-8000 Aarhus
> > Web: www.inano.au.dk<https://mail.au.dk/owa/UrlBlockedError.aspx>
> >
> > [
> >
> http://t2.gstatic.com/images?q=tbn:ANd9GcSuNO--QyrO9DDzk905MnRZxHFnNvip2292d5KqdHoryiDJgcsH
> > ]
> >
> >
> >
> > --
> > 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

Michael Elbaum

Re: Opening files from TIA software

Thanks Kenton (but the macro is missing !?!). The emi is a container for both images and spectroscopy, so for example if you take STEM images in bright and dark field you get XX_1.ser and XX_2.ser and the .emi is twice the size. There is no separate file for spectra. After opening with the TIA_Reader plugin, Image > Show info shows a number of parameters so metadata is present, but one never knows if some is missing.
regards,
Michael

________________________________________
From: ImageJ Interest Group [[hidden email]] on behalf of Kenton Arkill [[hidden email]]
Sent: Sunday, January 11, 2015 06:23
To: [hidden email]
Subject: Re: Opening files from TIA software

Here is the marco I use.
I normally have 2 files for each XX.emi and XX_1.ser. This macro gestured
of the _1.ser but a different version of the software might not have the _1
bit so will need altering. I've as yet not found a reason to keep the .emi
file afterwards. If you open the .tif as a text I think (I haven't checked)
that at the end is a list of microscope parameters which would have been in
the .emi, I've only used it when the scale became uncalibrated and had to
covert from the scope mag to actual scale....

Kenton

On 11 January 2015 at 04:01, Michael Elbaum <[hidden email]>
wrote:

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

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

Kenton Arkill

Re: Opening files from TIA software

I don't know how to attach files to the list so it is printed below.
----------------
// Macro to turn .ser's into .tif's

dir = getDirectory("Choose a Directory");
list = getFileList(dir);
setBatchMode(true);

showStatus("Running...");
for (i=0; i<list.length; i++) {
path = dir+list[i];

if(endsWith(path, ".ser")){
//Could be any ending like ".tif" !
run("TIA Reader", ".ser-reader...=path"); // Uses a plugin to open
// would be simply "open(path);" for normal image format
//----------------------------- CAN PUT ANY MANIPULTION BETWEEN HERE!!!!
dotIndex = lastIndexOf(path, ".");
//Finds the dot and therefore checks the file ends in .something
if (dotIndex!=-1){
path = substring(path, 0, dotIndex-2);
}
// finds 2 characters before dot to remove "_1.ser" extension
// for yours cut the -2 so it is just the extension so keep both versions
//---------------------------- AND HERE!!!!

save(path+".tif");// could add any ending like 'manipulation.tiff'
}
close();
}
}
showStatus("Done");
---------------

On 11 January 2015 at 13:12, Michael Elbaum <[hidden email]>
wrote:

> Thanks Kenton (but the macro is missing !?!). The emi is a container for
> both images and spectroscopy, so for example if you take STEM images in
> bright and dark field you get XX_1.ser and XX_2.ser and the .emi is twice
> the size. There is no separate file for spectra. After opening with the
> TIA_Reader plugin, Image > Show info shows a number of parameters so
> metadata is present, but one never knows if some is missing.
> regards,
> Michael
>
> ________________________________________
> From: ImageJ Interest Group [[hidden email]] on behalf of Kenton
> Arkill [[hidden email]]
> Sent: Sunday, January 11, 2015 06:23
> To: [hidden email]
> Subject: Re: Opening files from TIA software
>
> Here is the marco I use.
> I normally have 2 files for each XX.emi and XX_1.ser. This macro gestured
> of the _1.ser but a different version of the software might not have the _1
> bit so will need altering. I've as yet not found a reason to keep the .emi
> file afterwards. If you open the .tif as a text I think (I haven't checked)
> that at the end is a list of microscope parameters which would have been in
> the .emi, I've only used it when the scale became uncalibrated and had to
> covert from the scope mag to actual scale....
>
> Kenton
>
>
>
>
> On 11 January 2015 at 04:01, Michael Elbaum <[hidden email]
> >
> wrote:
>
> > I'm also using the plugin for .ser files, and re my earlier post about
> > opening multiple files it is in fact macro-compatible. (Thanks to Aryeh
> > Weiss and Nadav Elad.) It should be possible to have it open
> drag-and-drop
> > according to instructions in a comment in the java source file, by
> > modifying the HandleExtraFileTypes plugin. I didn't manage to make that
> > work, but it raises the question that maybe there's some other plugin
> > catching the .ser filetype on your system? Have you succeeded in adding
> > other plugins or do you get the same error?
> >
> > Kenton, any chance you could share the conversion macro? It would be very
> > helpful to many of us using TIA!
> >
> > Michael
> >
> > ________________________________________
> > From: ImageJ Interest Group [[hidden email]] on behalf of Kenton
> > Arkill [[hidden email]]
> > Sent: Saturday, January 10, 2015 06:50
> > To: [hidden email]
> > Subject: Re: Opening files from TIA software
> >
> > I don't know about the error. However the pluggin in the plugging folder
> > appears in the in-out sub folder in the plugins tree. It also opens the
> > .ser files not the .emi files. Personally I then have a macro that
> converts
> > a folder of .ser into tif. No information (headers etc) are lost.
> > Not the answer but might help...
> > Kenton
> > On Jan 10, 2015 11:29 AM, "Søren Roesgaard Nielsen" <
> [hidden email]
> > >
> > wrote:
> >
> > > Hi
> > >
> > > I am trying to open TEM files acuired using TIA software.
> > >
> > > The file is a .emi file.
> > >
> > > I have tried to install the following plugin:
> > > http://imagej.nih.gov/ij/plugins/tia-reader.html
> > >
> > > But I cannot get it to show up I Fiji, I gives the following error
> when I
> > > try to install it:
> > > WARNING: The PluginClassLoader cannot be reset
> > >
> > > Any suggestions?
> > >
> > > Søren Roesgaard Nielsen
> > > Ph.D. Student
> > > Tel.: +45 28 78 14 25
> > > Office: 1590-151
> > > Email: [hidden email]<mailto:[hidden email]>
> > >
> > > iNANO
> > > Aarhus University
> > > Gustav Wieds Vej 14
> > > DK-8000 Aarhus
> > > Web: www.inano.au.dk<https://mail.au.dk/owa/UrlBlockedError.aspx>
> > >
> > > [
> > >
> >
> http://t2.gstatic.com/images?q=tbn:ANd9GcSuNO--QyrO9DDzk905MnRZxHFnNvip2292d5KqdHoryiDJgcsH
> > > ]
> > >
> > >
> > >
> > > --
> > > 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
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

Jeff Stokes

Re: Opening files from TIA software

Is anyone aware of a macro or plugin for opening NITF files? Jeff Stokes

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Kenton
Arkill
Sent: Sunday, January 11, 2015 7:37 AM
To: [hidden email]
Subject: Re: Opening files from TIA software

I don't know how to attach files to the list so it is printed below.
----------------
// Macro to turn .ser's into .tif's

dir = getDirectory("Choose a Directory");
list = getFileList(dir);
setBatchMode(true);

showStatus("Running...");
for (i=0; i<list.length; i++) {
path = dir+list[i];

if(endsWith(path, ".ser")){
//Could be any ending like ".tif" !
run("TIA Reader", ".ser-reader...=path"); // Uses a plugin to open
// would be simply "open(path);" for normal image format
//----------------------------- CAN PUT ANY MANIPULTION BETWEEN HERE!!!!
dotIndex = lastIndexOf(path, ".");
//Finds the dot and therefore checks the file ends in .something
if (dotIndex!=-1){
path = substring(path, 0, dotIndex-2);
}
// finds 2 characters before dot to remove "_1.ser" extension
// for yours cut the -2 so it is just the extension so keep both versions
//---------------------------- AND HERE!!!!

save(path+".tif");// could add any ending like 'manipulation.tiff'
}
close();
}
}
showStatus("Done");
---------------

On 11 January 2015 at 13:12, Michael Elbaum <[hidden email]>
wrote:

_1
> bit so will need altering. I've as yet not found a reason to keep the .emi
> file afterwards. If you open the .tif as a text I think (I haven't
checked)
> that at the end is a list of microscope parameters which would have been
in

> the .emi, I've only used it when the scale became uncalibrated and had to
> covert from the scope mag to actual scale....
>
> Kenton
>
>
>
>
> On 11 January 2015 at 04:01, Michael Elbaum <[hidden email]
> >
> wrote:
>
> > I'm also using the plugin for .ser files, and re my earlier post about
> > opening multiple files it is in fact macro-compatible. (Thanks to Aryeh
> > Weiss and Nadav Elad.) It should be possible to have it open
> drag-and-drop
> > according to instructions in a comment in the java source file, by
> > modifying the HandleExtraFileTypes plugin. I didn't manage to make that
> > work, but it raises the question that maybe there's some other plugin
> > catching the .ser filetype on your system? Have you succeeded in adding
> > other plugins or do you get the same error?
> >
> > Kenton, any chance you could share the conversion macro? It would be

very

> > helpful to many of us using TIA!
> >
> > Michael
> >
> > ________________________________________
> > From: ImageJ Interest Group [[hidden email]] on behalf of Kenton
> > Arkill [[hidden email]]
> > Sent: Saturday, January 10, 2015 06:50
> > To: [hidden email]
> > Subject: Re: Opening files from TIA software
> >
> > I don't know about the error. However the pluggin in the plugging folder
> > appears in the in-out sub folder in the plugins tree. It also opens the
> > .ser files not the .emi files. Personally I then have a macro that
> converts
> > a folder of .ser into tif. No information (headers etc) are lost.
> > Not the answer but might help...
> > Kenton
> > On Jan 10, 2015 11:29 AM, "Søren Roesgaard Nielsen" <
> [hidden email]
> > >
> > wrote:
> >
> > > Hi
> > >
> > > I am trying to open TEM files acuired using TIA software.
> > >
> > > The file is a .emi file.
> > >
> > > I have tried to install the following plugin:
> > > http://imagej.nih.gov/ij/plugins/tia-reader.html
> > >
> > > But I cannot get it to show up I Fiji, I gives the following error
> when I
> > > try to install it:
> > > WARNING: The PluginClassLoader cannot be reset
> > >
> > > Any suggestions?
> > >
> > > Søren Roesgaard Nielsen
> > > Ph.D. Student
> > > Tel.: +45 28 78 14 25
> > > Office: 1590-151
> > > Email: [hidden email]<mailto:[hidden email]>
> > >
> > > iNANO
> > > Aarhus University
> > > Gustav Wieds Vej 14
> > > DK-8000 Aarhus
> > > Web: www.inano.au.dk<https://mail.au.dk/owa/UrlBlockedError.aspx>
> > >
> > > [
> > >
> >
>

http://t2.gstatic.com/images?q=tbn:ANd9GcSuNO--QyrO9DDzk905MnRZxHFnNvip2292d
5KqdHoryiDJgcsH

> > > ]
> > >
> > >
> > >
> > > --
> > > 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
>
> --
> 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

Herbie-4

Re: Opening files from TIA software

Jeff,

why not search the web for ImageJ & NITF?
<https://github.com/hobu/nitro/tree/master/java/nitf.imagej>

HTH

Herbie

:::::::::::::::::::::::::::::::::::::
On 12.01.15 09:25, Jeff Stokes wrote:
> Is anyone aware of a macro or plugin for opening NITF files? Jeff Stokes

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