question on opening Leica .lif file

[Lai Ding]

Hi,

  I have a question regarding LOCI open Leica .lif file.

  Is there a simple way or macro function to know the number of dataset in a .lif file without opening all of them?  

  I have some very large .lif file, I would like to open each individual dataset (labeled "series_x" ) in .lif file and save it as Tiff format.  I like to write a macro to do this task, but need to know the total number of dataset for the "for" loop.

 currently  I just open them all, and get the number from "nImages",  however sometimes the .lif is so big, that the RAM is not enough to handle the file.

 Thanks
Lai

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[ctrueden]

Hi Lai,

> Is there a simple way or macro function to know the number of dataset
> in a .lif file without opening all of them?

Here's a macro:

run("Bio-Formats Macro Extensions");
file = File.openDialog("Choose a file");
Ext.setId(file);
Ext.getSeriesCount(seriesCount);
showMessage("Dataset has " + seriesCount + " images");

Regards,
Curtis


On Wed, Dec 17, 2014 at 9:41 AM, Lai Ding <[hidden email]> wrote:

>
> Hi,
>
>   I have a question regarding LOCI open Leica .lif file.
>
>   Is there a simple way or macro function to know the number of dataset in
> a .lif file without opening all of them?
>
>   I have some very large .lif file, I would like to open each individual
> dataset (labeled "series_x" ) in .lif file and save it as Tiff format.  I
> like to write a macro to do this task, but need to know the total number of
> dataset for the "for" loop.
>
>  currently  I just open them all, and get the number from "nImages",
> however sometimes the .lif is so big, that the RAM is not enough to handle
> the file.
>
>  Thanks
> Lai
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

... [show rest of quote]

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

[Lai Ding]

Thanks Curtis.

This is  exactly what I need.

Best
Lai

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Curtis Rueden
Sent: Wednesday, December 17, 2014 11:41 AM
To: [hidden email]
Subject: Re: question on opening Leica .lif file

Hi Lai,

> Is there a simple way or macro function to know the number of dataset
> in a .lif file without opening all of them?

Here's a macro:

run("Bio-Formats Macro Extensions");
file = File.openDialog("Choose a file"); Ext.setId(file); Ext.getSeriesCount(seriesCount); showMessage("Dataset has " + seriesCount + " images");

Regards,
Curtis


On Wed, Dec 17, 2014 at 9:41 AM, Lai Ding <[hidden email]> wrote:

>
> Hi,
>
>   I have a question regarding LOCI open Leica .lif file.
>
>   Is there a simple way or macro function to know the number of
> dataset in a .lif file without opening all of them?
>
>   I have some very large .lif file, I would like to open each
> individual dataset (labeled "series_x" ) in .lif file and save it as
> Tiff format.  I like to write a macro to do this task, but need to
> know the total number of dataset for the "for" loop.
>
>  currently  I just open them all, and get the number from "nImages",
> however sometimes the .lif is so big, that the RAM is not enough to
> handle the file.
>
>  Thanks
> Lai
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

... [show rest of quote]

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

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