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make transparent images

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kirstens

make transparent images

Hi there,

I've got images of fluorescent particles that I have run through a pipeline involving deconvolution, watershed algorithm and analyze particles. I have binary images as part of the output.

In order to provide a check I wanted to overlay these back onto the original images. I can easily overlay the original image using edit>overlay but I can't seem to set the transparency of the top image so that you can see both at the same time.

I tried to download Michael Schmid's alpha channel plug-in but I"ve not been able to get it to compile (keep getting errors) (see http://imagejdocu.tudor.lu/doku.php?id=plugin:utilities:alpha_channel:start).

It seems that this is probably a simple procedure so I imagine I've missed something.

Has anyone else had a similar problem?

Kirsten

___________________
Kirsten Scott
Academic Clinical Fellow Addenbrooke's Hospital/
Wellcome Trust Sanger Centre

G. Esteban Fernandez

Re: make transparent images

What about Image > Color > Merge Channels? Use the original as Gray
and the binary as one of the colors (green shows up well). Depending
on how bright the original is, you might have to darken it to see the
color better.

-Esteban

On Thu, Sep 1, 2011 at 6:27 AM, Kirsten Scott <[hidden email]> wrote:

> Hi there,
>
> I've got images of fluorescent particles that I have run through a pipeline involving deconvolution, watershed algorithm and analyze particles. I have binary images as part of the output.
>
> In order to provide a check I wanted to overlay these back onto the original images. I can easily overlay the original image using edit>overlay but I can't seem to set the transparency of the top image so that you can see both at the same time.
>
> I tried to download Michael Schmid's alpha channel plug-in but I"ve not been able to get it to compile (keep getting errors) (see http://imagejdocu.tudor.lu/doku.php?id=plugin:utilities:alpha_channel:start).
>
> It seems that this is probably a simple procedure so I imagine I've missed something.
>
> Has anyone else had a similar problem?
>
> Kirsten
>
> ___________________
> Kirsten Scott
> Academic Clinical Fellow Addenbrooke's Hospital/
> Wellcome Trust Sanger Centre
>

Michael Schmid

Re: make transparent images

In reply to this post by kirstens

Hi Kirsten,

using ImageJ 1.45l I can still compile the 'Alpha Channel' plugin. Please make sure that the file is named exactly "Alpha_Channel.java"; uppercase and lowercase matters (unfortunately, everything gets converted to lowercase by the DokuWiki system used at imagejdocu.tudor.lu).

Anyhow, if you have a binary image and you want to see it as an overlay, the easiest option is converting it to a roi (Edit>Selection>Create Selection) and then transferring it to the input image of your processing. You can do this via the ROI manager or (more simply) by selecting the input image and simply typing shift-E ('restore selection').

Then you can also use Image>Overlay>Add Selection to create it into an overlay that is independent of the selection; with either the foreground area filled or the outline marked.

Still another possibility is Image>Overlay>Add Image, where you can have a transparent overlay. In contrast to the Alpha Channel plugin, all these Overlays are nondestructive, i.e., they don't modify the image data and are stored separately from the image data if you save the image as tiff or zip.

Michael
______________________________________________________________
On 2011-Sep-01, at 15:27, Kirsten Scott wrote: