Re: Creating individual tiles from one large image

Posted by Jacqueline Ross on
URL: http://imagej.273.s1.nabble.com/Creating-individual-tiles-from-one-large-image-tp5000374p5000424.html

Dear Curtis, Christian, Johannes & John,

Thanks very much to each of you for your suggestions. The easiest method is the one suggested by Christian so I think the students can use that method since it doesn't really matter if the tiles are a certain size.

I haven't yet managed to get the other methods working properly but haven't had much time this week to pursue them properly.

I hope it's OK to come back to you if I have further questions.

Thanks!

Kind regards,

Jacqui

Jacqueline Ross
Biomedical Imaging Microscopist
Biomedical Imaging Research Unit 
School of Medical Sciences 
Faculty of Medical & Health Sciences
The University of Auckland
Private Bag 92019
Auckland 1142, NEW ZEALAND

Tel: [phone]
Fax: [phone]

http://www.fmhs.auckland.ac.nz/sms/biru/


-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Curtis Rueden
Sent: Friday, 12 October 2012 6:10 a.m.
To: [hidden email]
Subject: Re: Creating individual tiles from one large image

Hi Jacqui,

> So what we need to do is divide the large image into separate tiles
> and output them as an image sequence.

You can also do this using the Bio-Formats command line tools:
   http://loci.wisc.edu/bio-formats/command-line-tools

You would use a series of calls to the "bfconvert" command line tool with the "-crop" option to create tiles sized to your liking; e.g., "-crop 0,0,512,512", "-crop 512,0,512,512", etc., up to the size of your planes in
2 dimensions.

Regards,
Curtis


On Thu, Oct 11, 2012 at 12:22 AM, Jacqui Ross <[hidden email]>wrote:

> Hi All,
>
> We have a slide-scanner which images sequentially across a tissue
> section and then creates a large composite tiled image. We can output
> the files as individual tiles as well in RAW format.
>
> However, I am attempting to assist a few students who have deleted the
> individual tile files and now want to divide their images into
> individual tiles (e.g.512 x 512 pixels) for the analysis.
>
> So what we need to do is divide the large image into separate tiles
> and output them as an image sequence.
>
> I thought I could do it by creating rectangles and cropping or
> duplicating but can't work out how to get it working across the entire
> image. Can anyone help me with this?
>
> I'm starting to think it might be easier to rescan the sections and
> get the raw data again!
>
> Kind regards,
>
> Jacqui
>
> Jacqueline Ross
> Biomedical Imaging Microscopist
> Biomedical Imaging Research Unit
> School of Medical Sciences
> Faculty of Medical & Health Sciences
> The University of Auckland
> Private Bag 92019
> Auckland 1142, NEW ZEALAND
>
> Tel: [phone]
> Fax: [phone]
>
> http://www.fmhs.auckland.ac.nz/sms/biru/
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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