Reading nd2 Hyperstacks from jython

[Greg]

Hi,

thanks to this script here https://gist.github.com/ctrueden/6282856 I can read in nd2 Hyperstacks into Fiji in headless mode with jython.
I am just a bit baffled that the Read_Image function returns an array. Right now I am reading in a 'one-frame,one-slice,three-channel) hyperstack, so I just do

imp = BF.openImagePlus(dirpath + name )[0]

and I think I get the correct ImagePlus loaded. I wonder what the indices of the array actually indexes, I can not find a good documentation of the Bioformats API, and reading the plugin code

https://github.com/openmicroscopy/bioformats/blob/v4.4.12/components/loci-plugins/utils/Read_Image.java

does not answer this question for me.

Best,
Greg

[ctrueden]

Hi Greg,

The best place for Bio-Formats question is the OME Users list [1].

> I wonder what the indices of the array actually indexes,

Some file formats support storing more than one 5-dimensional block of
pixels in the same dataset. For example, each Leica LIF file is an entire
"experiment" that can contain any number of what Bio-Formats calls "image
series." In the ImageJ API, each such "image series" is returned as a
separate ImagePlus.

Regards,
Curtis

[1] http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users/

On Mon, Mar 30, 2015 at 7:13 AM, Greg <[hidden email]> wrote:

> Hi,
>
> thanks to this script here https://gist.github.com/ctrueden/6282856 I can
> read in nd2 Hyperstacks into Fiji in headless mode with jython.
> I am just a bit baffled that the Read_Image function returns an array.
> Right
> now I am reading in a 'one-frame,one-slice,three-channel) hyperstack, so I
> just do
>
> imp = BF.openImagePlus(dirpath + name )[0]
>
> and I think I get the correct ImagePlus loaded. I wonder what the indices
> of
> the array actually indexes, I can not find a good documentation of the
> Bioformats API, and reading the plugin code
>
>
> https://github.com/openmicroscopy/bioformats/blob/v4.4.12/components/loci-plugins/utils/Read_Image.java
>
> does not answer this question for me.
>
> Best,
> Greg
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/Reading-nd2-Hyperstacks-from-jython-tp5012249.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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