IMS files - open with duplicated file name

[Jacqueline Ross]

Hi everyone,

We have a MetaSystems VSlide slide-scanner that has an option to extract files as IMS (Imaris) format. I prefer to use this because it is a hierarchy system where you can choose the resolution level that you need for analysis without having to use the full resolution unless you need to.

However, the file name is duplicated which makes things a bit tricky. Does anyone know how to fix this, e.g. is it something to do with the options I have selected for the Bioformats importer? It's the same for files that come directly from Imaris.

I have attached the log file that has the title of the image listed and a snip of the image details at the top of the image window.

Another option is for me to run a "rename" step that takes the additional characters out but I'm not sure how to do this...

Any help would be much appreciated.

Kind regards,

Jacqui

Jacqueline Ross
Lead Technologist
Optical Microscopy & Image Analysis
Biomedical Imaging Research Unit (BIRU)
School of Medical Sciences
Faculty of Medical & Health Sciences
The University of Auckland
Private Bag 92019
Auckland 1142, NEW ZEALAND

Telephone: Ext 87438; DDI:  [phone]

Website:    http://www.auckland.ac.nz/biru




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[jmutterer]

Hi Jacqui,

You could save the following macro as "rename_ims_image.ijm" in the plugins
folder

t=getTitle();
rename(t.substring( 0,t.lastIndexOf(t.substring(0,t.indexOf(".ims")+4))-3));

And this will give you a "rename ims image" command in the plugins menu.
You can then call it from the menu, or using:
run("rename ims image");
in a script.


Jerome.



On Tue, 22 Dec 2020 at 06:11, Jacqueline Ross <[hidden email]>
wrote:

> Hi everyone,
>
> We have a MetaSystems VSlide slide-scanner that has an option to extract
> files as IMS (Imaris) format. I prefer to use this because it is a
> hierarchy system where you can choose the resolution level that you need
> for analysis without having to use the full resolution unless you need to.
>
> However, the file name is duplicated which makes things a bit tricky. Does
> anyone know how to fix this, e.g. is it something to do with the options I
> have selected for the Bioformats importer? It's the same for files that
> come directly from Imaris.
>
> I have attached the log file that has the title of the image listed and a
> snip of the image details at the top of the image window.
>
> Another option is for me to run a "rename" step that takes the additional
> characters out but I'm not sure how to do this...
>
> Any help would be much appreciated.
>
> Kind regards,
>
> Jacqui
>
> Jacqueline Ross
> Lead Technologist
> Optical Microscopy & Image Analysis
> Biomedical Imaging Research Unit (BIRU)
> School of Medical Sciences
> Faculty of Medical & Health Sciences
> The University of Auckland
> Private Bag 92019
> Auckland 1142, NEW ZEALAND
>
> Telephone: Ext 87438; DDI:  [phone]
>
> Website:    http://www.auckland.ac.nz/biru
>
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[jmutterer]

Hi again!
Here's a simpler version that also works :-)

t=getTitle();
rename(t.substring(0,t.indexOf(".ims")+4));

On Tue, 22 Dec 2020 at 12:49, Jerome Mutterer <[hidden email]>
wrote:

> Hi Jacqui,
>
> You could save the following macro as "rename_ims_image.ijm" in the
> plugins folder
>
> t=getTitle();
> rename(t.substring(
> 0,t.lastIndexOf(t.substring(0,t.indexOf(".ims")+4))-3));
>
> And this will give you a "rename ims image" command in the plugins menu.
> You can then call it from the menu, or using:
> run("rename ims image");
> in a script.
>
>
> Jerome.
>
>
>
> On Tue, 22 Dec 2020 at 06:11, Jacqueline Ross <[hidden email]>
> wrote:
>
>> Hi everyone,
>>
>> We have a MetaSystems VSlide slide-scanner that has an option to extract
>> files as IMS (Imaris) format. I prefer to use this because it is a
>> hierarchy system where you can choose the resolution level that you need
>> for analysis without having to use the full resolution unless you need to.
>>
>> However, the file name is duplicated which makes things a bit tricky.
>> Does anyone know how to fix this, e.g. is it something to do with the
>> options I have selected for the Bioformats importer? It's the same for
>> files that come directly from Imaris.
>>
>> I have attached the log file that has the title of the image listed and a
>> snip of the image details at the top of the image window.
>>
>> Another option is for me to run a "rename" step that takes the additional
>> characters out but I'm not sure how to do this...
>>
>> Any help would be much appreciated.
>>
>> Kind regards,
>>
>> Jacqui
>>
>> Jacqueline Ross
>> Lead Technologist
>> Optical Microscopy & Image Analysis
>> Biomedical Imaging Research Unit (BIRU)
>> School of Medical Sciences
>> Faculty of Medical & Health Sciences
>> The University of Auckland
>> Private Bag 92019
>> Auckland 1142, NEW ZEALAND
>>
>> Telephone: Ext 87438; DDI:  [phone]
>>
>> Website:    http://www.auckland.ac.nz/biru
>>
>>
>>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>

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

[Jacqueline Ross]

Hi Jerome,

Thank you so much. This works perfectly and has solved my problem.

Cheers,

Jacqui

From: ImageJ Interest Group <[hidden email]> On Behalf Of Jerome Mutterer
Sent: Wednesday, December 23, 2020 12:55 AM
To: [hidden email]
Subject: Re: IMS files - open with duplicated file name

Hi again!
Here's a simpler version that also works :-)

t=getTitle();
rename(t.substring(0,t.indexOf(".ims")+4));

On Tue, 22 Dec 2020 at 12:49, Jerome Mutterer <[hidden email]<mailto:[hidden email]>>
wrote:

> Hi Jacqui,
>
> You could save the following macro as "rename_ims_image.ijm" in the
> plugins folder
>
> t=getTitle();
> rename(t.substring(
> 0,t.lastIndexOf(t.substring(0,t.indexOf(".ims")+4))-3));
>
> And this will give you a "rename ims image" command in the plugins menu.
> You can then call it from the menu, or using:
> run("rename ims image");
> in a script.
>
>
> Jerome.
>
>
>
> On Tue, 22 Dec 2020 at 06:11, Jacqueline Ross <[hidden email]<mailto:[hidden email]>>
> wrote:
>
>> Hi everyone,
>>
>> We have a MetaSystems VSlide slide-scanner that has an option to extract
>> files as IMS (Imaris) format. I prefer to use this because it is a
>> hierarchy system where you can choose the resolution level that you need
>> for analysis without having to use the full resolution unless you need to.
>>
>> However, the file name is duplicated which makes things a bit tricky.
>> Does anyone know how to fix this, e.g. is it something to do with the
>> options I have selected for the Bioformats importer? It's the same for
>> files that come directly from Imaris.
>>
>> I have attached the log file that has the title of the image listed and a
>> snip of the image details at the top of the image window.
>>
>> Another option is for me to run a "rename" step that takes the additional
>> characters out but I'm not sure how to do this...
>>
>> Any help would be much appreciated.
>>
>> Kind regards,
>>
>> Jacqui
>>
>> Jacqueline Ross
>> Lead Technologist
>> Optical Microscopy & Image Analysis
>> Biomedical Imaging Research Unit (BIRU)
>> School of Medical Sciences
>> Faculty of Medical & Health Sciences
>> The University of Auckland
>> Private Bag 92019
>> Auckland 1142, NEW ZEALAND
>>
>> Telephone: Ext 87438; DDI: [phone]
>>
>> Website: http://www.auckland.ac.nz/biru<http://www.auckland.ac.nz/biru>
>>
>>
>>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html<http://imagej.nih.gov/ij/list.html>
>>
>

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

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