Using the Bioformats importer to open .ims files in a macro

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Using the Bioformats importer to open .ims files in a macro

Jacqueline Ross
Hi everyone,

Our slide-scanner has an option to save files as .ims (Imaris) format. This allows us to open the files in ImageJ at different resolution levels.

I'm trying to write a macro that will open the files at "Resolution Level 2" rather than Level 1 (which is the highest) and just can't seem to get this to work.

Has anyone done this already and is willing to share the code?

It would be similar for those opening Leica .lif files where you can select the Series number.

Thanks!

Kind regards,

Jacqui

Jacqueline Ross
Biomedical Imaging Microscopist
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:  +64 9 923 7438

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




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Re: Using the Bioformats importer to open .ims files in a macro

David Gault (Staff)
Hi Jacqueline,

You can find some examples of Bio-Formats macros at https://docs.openmicroscopy.org/bio-formats/5.8.2/users/imagej/#macros-and-plugins
To select the other resolutions you will need to set the Series, using Ext.setSeries(seriesNum) as in https://github.com/openmicroscopy/bioformats/blob/develop/components/bio-formats-plugins/utils/macros/basicMetadata.txt

With Thanks,
David Gault

On 19 Sep 2018, at 01:59, Jacqueline Ross <[hidden email]<mailto:[hidden email]>> wrote:

Hi everyone,

Our slide-scanner has an option to save files as .ims (Imaris) format. This allows us to open the files in ImageJ at different resolution levels.

I'm trying to write a macro that will open the files at "Resolution Level 2" rather than Level 1 (which is the highest) and just can't seem to get this to work.

Has anyone done this already and is willing to share the code?

It would be similar for those opening Leica .lif files where you can select the Series number.

Thanks!

Kind regards,

Jacqui

Jacqueline Ross
Biomedical Imaging Microscopist
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:  +64 9 923 7438

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




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The University of Dundee is a registered Scottish Charity, No: SC015096

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Re: Using the Bioformats importer to open .ims files in a macro

Jacqueline Ross
Hi David,

Thanks very much for your reply. I had looked at the first link you sent previously but couldn't see how to integrate the Series option. I still haven't succeeded though I have tried Curtis's macro to get the Series number. I want number 2 but it's not working currently.

I'll have to persevere but if you were able to send  me a simple example, it would be great.

All I need to be able to do is open the file at resolution level 2 as level 1 is too large to process.

Kind regards,

Jacqui

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of David Gault (Staff)
Sent: Wednesday, 19 September 2018 9:32 p.m.
To: [hidden email]
Subject: Re: Using the Bioformats importer to open .ims files in a macro

Hi Jacqueline,

You can find some examples of Bio-Formats macros at https://docs.openmicroscopy.org/bio-formats/5.8.2/users/imagej/#macros-and-plugins
To select the other resolutions you will need to set the Series, using Ext.setSeries(seriesNum) as in https://github.com/openmicroscopy/bioformats/blob/develop/components/bio-formats-plugins/utils/macros/basicMetadata.txt

With Thanks,
David Gault

On 19 Sep 2018, at 01:59, Jacqueline Ross <[hidden email]<mailto:[hidden email]>> wrote:

Hi everyone,

Our slide-scanner has an option to save files as .ims (Imaris) format. This allows us to open the files in ImageJ at different resolution levels.

I'm trying to write a macro that will open the files at "Resolution Level 2" rather than Level 1 (which is the highest) and just can't seem to get this to work.

Has anyone done this already and is willing to share the code?

It would be similar for those opening Leica .lif files where you can select the Series number.

Thanks!

Kind regards,

Jacqui

Jacqueline Ross
Biomedical Imaging Microscopist
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:  +64 9 923 7438

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




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


The University of Dundee is a registered Scottish Charity, No: SC015096

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Re: Using the Bioformats importer to open .ims files in a macro

Rocco D'Antuono
Hi Jacqueline, this code opens the second series in your file (tested at
least in ".lif" file).
Obviously you can change the value of "series_number" to select other images
in the list.
Best,
Rocco

---------------------------------------------------
/pathToFile = File.openDialog("Choose a file");
print(pathToFile);
series_number=2;
run("Bio-Formats Importer", "open=["+pathToFile+"] color_mode=Default
rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT
series_"+series_number+"");/
---------------------------------------------------



-----
Senior Microscopist
Crick Advanced Light Microscopy facility (CALM)
The Francis Crick Institute
1 Midland Road, NW1 1AT, London (UK)
--
Sent from: http://imagej.1557.x6.nabble.com/

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Senior Microscopist
Crick Advanced Light Microscopy facility (CALM)
The Francis Crick Institute
1 Midland Road, NW1 1AT, London (UK)
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Re: Using the Bioformats importer to open .ims files in a macro

Jacqueline Ross
Hi Rocco,
Thank you so much for that code. It looks like just what I need. I am on leave at present but will try it out as soon as I return.
Cheers,
Jacqui
________________________________________
From: ImageJ Interest Group [[hidden email]] on behalf of Rocco D'Antuono [[hidden email]]
Sent: 22 September 2018 04:40
To: [hidden email]
Subject: Re: Using the Bioformats importer to open .ims files in a macro

Hi Jacqueline, this code opens the second series in your file (tested at
least in ".lif" file).
Obviously you can change the value of "series_number" to select other images
in the list.
Best,
Rocco

---------------------------------------------------
/pathToFile = File.openDialog("Choose a file");
print(pathToFile);
series_number=2;
run("Bio-Formats Importer", "open=["+pathToFile+"] color_mode=Default
rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT
series_"+series_number+"");/
---------------------------------------------------



-----
Senior Microscopist
Crick Advanced Light Microscopy facility (CALM)
The Francis Crick Institute
1 Midland Road, NW1 1AT, London (UK)
--
Sent from: http://imagej.1557.x6.nabble.com/

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

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