How to Batch Threshold, Crop & Save multi-page tiffs?

[Francis]

Hello

I am a complete newbie to ImageJ but I am trying to figure out how to batch threshold, crop and save an entire folder of 100's multi-page tiff files (each tiff has 1000 individual images). This would greatly reduce the current file size and make it much easier to start analysing the images.

Does have any advice or directions on to do this? I would really appreciate any help that people can provide.

Best,

Albert

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[ctrueden]

Hi Albert,

> I am trying to figure out how to batch threshold, crop and save an
> entire folder of 100's multi-page tiff files

You can record a macro [1] of yourself performing the relevant tasks, then
tweak the resulting macro for your needs. You can then execute it en masse
using the Process > Batch > Macro... command [2], or by looping over all
your TIFFs in the macro itself [3].

Regards,
Curtis

[1] http://fiji.sc/Introduction_into_Macro_Programming#The_recorder
[2]
http://rsbweb.nih.gov/ij/docs/guide/146-29.html#toc-Subsubsection-29.12.3
[3] E.g.:
https://github.com/openmicroscopy/bioformats/blob/v4.4.9/components/loci-plugins/utils/macros/batchTiffConvert.txt


On Tue, Nov 12, 2013 at 2:05 PM, Albert James
<[hidden email]>wrote:

> Hello
>
> I am a complete newbie to ImageJ but I am trying to figure out how to
> batch threshold, crop and save an entire folder of 100's multi-page tiff
> files (each tiff has 1000 individual images). This would greatly reduce the
> current file size and make it much easier to start analysing the images.
>
> Does have any advice or directions on to do this? I would really
> appreciate any help that people can provide.
>
> Best,
>
> Albert
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[Antoinette]

Hi, you need to apply and activate batch tiff reading and processing toolkits. We know, tiff file is a multi-page document, and when we are about to edit and save it, we need to use batch mode to crop and save tiff images.