Metadata in multi-position datasets

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Metadata in multi-position datasets

David Barry

Hello All,

 

We’re having some difficulty with the reading of metadata in multi-position datasets from MM2.

 

Essentially, it appears that, in such datasets, complete metadata is only stored in the first file in the series – is this correct?

 

This presents problems when attempting to, for example, open individual stacks from the dataset in Huygens, as the metadata in individual TIF stacks is incomplete and Huygens therefore reads and presents the data incorrectly.

 

Is there any way around this problem?

 

Thanks,

 

Dave.

 

 

Dave Barry,

Image Analyst,

Crick Advanced Light Microscopy Facility (CALM),

The Francis Crick Institute,

1 Midland Road,

London,

NW1 1AT.

 

T: +44 20379 60913

E: [hidden email]

W: www.crick.ac.uk

R: SW312

 

The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT



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Re: Metadata in multi-position datasets

David Barry

Hi,

 

Just following up on my below email. As mentioned previously, we’re having problems with Huygens reading multi-position datasets from MM2, as it would appear the metadata does not conform to the official OME TIFF guidelines.

 

This means we have to convert data (i.e. open in FIJI and resave) before it can be read by Huygens, which is not terribly convenient.

 

Is there a more convenient way around this problem?

 

Thanks,

 

Dave.

 

 

From: David Barry
Sent: 05 November 2018 14:42
To: [hidden email]
Subject: Metadata in multi-position datasets

 

Hello All,

 

We’re having some difficulty with the reading of metadata in multi-position datasets from MM2.

 

Essentially, it appears that, in such datasets, complete metadata is only stored in the first file in the series – is this correct?

 

This presents problems when attempting to, for example, open individual stacks from the dataset in Huygens, as the metadata in individual TIF stacks is incomplete and Huygens therefore reads and presents the data incorrectly.

 

Is there any way around this problem?

 

Thanks,

 

Dave.

 

 

Dave Barry,

Image Analyst,

Crick Advanced Light Microscopy Facility (CALM),

The Francis Crick Institute,

1 Midland Road,

London,

NW1 1AT.

 

T: +44 20379 60913

E: [hidden email]

W: www.crick.ac.uk

R: SW312

 

The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT



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Re: Metadata in multi-position datasets

Peter Braubach

Hi,

this issue was discussed on the ML before and Nick Anthony submitted a fix. I followed this because I too have troubles with this issue – and loading and resaving gigabytes of data is inconvenient.

 

https://github.com/micro-manager/micro-manager/pull/658

 

I do not know if this has found its way into the nightly builds

 

Kind regards

Peter

 

--

Dr. med. Peter Braubach

Koordinator Lungengewebebank

Arbeitsgruppe Lungenforschung

 

Institut für Pathologie

Medizinische Hochschule Hannover

OE 5110, Carl-Neuberg-Str. 1, 30625 Hannover, Deutschland

Tel.: +49 511 532-8494

[hidden email]

www.mh-hannover.de

 

Von: David Barry [mailto:[hidden email]]
Gesendet: Montag, 11. März 2019 16:34
An: [hidden email]
Betreff: Re: [micro-manager-general] Metadata in multi-position datasets

 

Hi,

 

Just following up on my below email. As mentioned previously, we’re having problems with Huygens reading multi-position datasets from MM2, as it would appear the metadata does not conform to the official OME TIFF guidelines.

 

This means we have to convert data (i.e. open in FIJI and resave) before it can be read by Huygens, which is not terribly convenient.

 

Is there a more convenient way around this problem?

 

Thanks,

 

Dave.

 

 

From: David Barry
Sent: 05 November 2018 14:42
To: [hidden email]
Subject: Metadata in multi-position datasets

 

Hello All,

 

We’re having some difficulty with the reading of metadata in multi-position datasets from MM2.

 

Essentially, it appears that, in such datasets, complete metadata is only stored in the first file in the series – is this correct?

 

This presents problems when attempting to, for example, open individual stacks from the dataset in Huygens, as the metadata in individual TIF stacks is incomplete and Huygens therefore reads and presents the data incorrectly.

 

Is there any way around this problem?

 

Thanks,

 

Dave.

 

 

Dave Barry,

Image Analyst,

Crick Advanced Light Microscopy Facility (CALM),

The Francis Crick Institute,

1 Midland Road,

London,

NW1 1AT.

 

T: +44 20379 60913

E: [hidden email]

W: www.crick.ac.uk

R: SW312

 

The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT



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Re: Metadata in multi-position datasets

David Barry

Thanks for that Peter, but that fix appears to be specific to the Acquire Multiple Regions Plugin?

 

Our users typically specify specific positions via Edit Position List in Multi-Dimensional Acquisition.

 

 

 

From: [hidden email] <[hidden email]>
Sent: 14 March 2019 09:51
To: [hidden email]
Subject: Re: [micro-manager-general] Metadata in multi-position datasets

 

Hi,

this issue was discussed on the ML before and Nick Anthony submitted a fix. I followed this because I too have troubles with this issue – and loading and resaving gigabytes of data is inconvenient.

 

https://github.com/micro-manager/micro-manager/pull/658

 

I do not know if this has found its way into the nightly builds

 

Kind regards

Peter

 

--

Dr. med. Peter Braubach

Koordinator Lungengewebebank

Arbeitsgruppe Lungenforschung

 

Institut für Pathologie

Medizinische Hochschule Hannover

OE 5110, Carl-Neuberg-Str. 1, 30625 Hannover, Deutschland

Tel.: +49 511 532-8494

[hidden email]

www.mh-hannover.de

 

Von: David Barry [[hidden email]]
Gesendet: Montag, 11. März 2019 16:34
An: [hidden email]
Betreff: Re: [micro-manager-general] Metadata in multi-position datasets

 

Hi,

 

Just following up on my below email. As mentioned previously, we’re having problems with Huygens reading multi-position datasets from MM2, as it would appear the metadata does not conform to the official OME TIFF guidelines.

 

This means we have to convert data (i.e. open in FIJI and resave) before it can be read by Huygens, which is not terribly convenient.

 

Is there a more convenient way around this problem?

 

Thanks,

 

Dave.

 

 

From: David Barry
Sent: 05 November 2018 14:42
To: [hidden email]
Subject: Metadata in multi-position datasets

 

Hello All,

 

We’re having some difficulty with the reading of metadata in multi-position datasets from MM2.

 

Essentially, it appears that, in such datasets, complete metadata is only stored in the first file in the series – is this correct?

 

This presents problems when attempting to, for example, open individual stacks from the dataset in Huygens, as the metadata in individual TIF stacks is incomplete and Huygens therefore reads and presents the data incorrectly.

 

Is there any way around this problem?

 

Thanks,

 

Dave.

 

 

Dave Barry,

Image Analyst,

Crick Advanced Light Microscopy Facility (CALM),

The Francis Crick Institute,

1 Midland Road,

London,

NW1 1AT.

 

T: +44 20379 60913

E: [hidden email]

W: www.crick.ac.uk

R: SW312

 

The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT

The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT



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Re: Metadata in multi-position datasets

Stuurman, Nico
In reply to this post by David Barry
Hi David,

On 3/11/2019 8:33 AM, David Barry wrote:
Just following up on my below email. As mentioned previously, we’re having problems with Huygens reading multi-position datasets from MM2, as it would appear the metadata does not conform to the official OME TIFF guidelines.

This means we have to convert data (i.e. open in FIJI and resave) before it can be read by Huygens, which is not terribly convenient.


I am not aware of anyone working on the file saving code right now.  Why don't you ask SVI to fix their reader?  You pay them money after all;)

Best,


Nico

 




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Re: Metadata in multi-position datasets

David Barry

Hi Nico,

 

I’ve been in correspondence with SVI and they’ve said they’re not willing to deviate from the official OME-TIF standard.

 

I guess we’ll just have to come up with a fix ourselves!

 

Dave.

 

 

From: Stuurman, Nico <[hidden email]>
Sent: 15 March 2019 03:29
To: Micro-Manager General <[hidden email]>
Subject: Re: [micro-manager-general] Metadata in multi-position datasets

 

Hi David,

On 3/11/2019 8:33 AM, David Barry wrote:

Just following up on my below email. As mentioned previously, we’re having problems with Huygens reading multi-position datasets from MM2, as it would appear the metadata does not conform to the official OME TIFF guidelines.

This means we have to convert data (i.e. open in FIJI and resave) before it can be read by Huygens, which is not terribly convenient.


I am not aware of anyone working on the file saving code right now.  Why don't you ask SVI to fix their reader?  You pay them money after all;)

Best,


Nico


 

 

The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT



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