Process Image Series File as Virtual Stack

[Sebastian Rhode-5]

Hi,

I have a tile image (.czi). When I read this via BioFormats, every tile is treated as an distinct image series. So in case of a 10x10 Tile, one ends up with 100 image series. Since the file is quite large, I want to the following:

- load 1st image series from complete data set (as virtual stack?)
- process 1st series
- save 1st series
- loop the whole thing

As a result I would still need one big image data set that can be saved as on ome-tiff and that contains 100 image series. Can someone point me into the right direction?

Sebi

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[ctrueden]

Hi Sebi,

Did you try the option "Concatenate series when compatible"? As long as
each image series has the same dimensions, it should smush them all
together into one big hyperstack. However, this option cannot be combined
with "Use virtual stack" right now, so you must have enough RAM to load it
all at once. If you do not have enough RAM, then you can write a macro or
script to loop over each image series, loading it one by one, and process
each series/tile individually.

> I would still need one big image data set that can be saved as on
> ome-tiff and that contains 100 image series.

If all you want is to convert .czi to .ome.tiff, preserving the separate
image series, you can just use the bfconvert tool. Or do I misunderstand
what you need here?

Regards,
Curtis

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Curtis Rueden
LOCI software architect - http://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
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On Tue, Jun 7, 2016 at 3:56 AM, Sebastian Rhode <
[hidden email]> wrote:

> Hi,
>
> I have a tile image (.czi). When I read this via BioFormats, every tile is
> treated as an distinct image series. So in case of a 10x10 Tile, one ends
> up with 100 image series. Since the file is quite large, I want to the
> following:
>
> - load 1st image series from complete data set (as virtual stack?)
> - process 1st series
> - save 1st series
> - loop the whole thing
>
> As a result I would still need one big image data set that can be saved as
> on ome-tiff and that contains 100 image series. Can someone point me into
> the right direction?
>
> Sebi
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[lartaud marc]

Hi,
Have you try to apply stitching process in Zen before saving in czi
format ?
Marc

Le 07/06/2016 à 10:56, Sebastian Rhode a écrit :

> Hi,
>
> I have a tile image (.czi). When I read this via BioFormats, every tile is treated as an distinct image series. So in case of a 10x10 Tile, one ends up with 100 image series. Since the file is quite large, I want to the following:
>
> - load 1st image series from complete data set (as virtual stack?)
> - process 1st series
> - save 1st series
> - loop the whole thing
>
> As a result I would still need one big image data set that can be saved as on ome-tiff and that contains 100 image series. Can someone point me into the right direction?
>
> Sebi
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[Sebastian Rhode-5]

Hi Marc,

yes, I did. And this works fine as along as the resulting image size is not huge. But when you have a let´s say 300GB TileImage, the stitched and fused (!) image exported from ZEN will be something Fiji will not really like ...

And when the large image results from something like a 384 plate with x independent positions per well, the stitching does not make sense anyway.

Cheers, Sebi

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