Re: FIJI 2D stitching in a macro - solution!

Posted by Jacqueline Ross on Nov 22, 2010; 11:23pm
URL: http://imagej.273.s1.nabble.com/FIJI-2D-stitching-in-a-macro-solution-tp3686366p3686368.html

Hi Christophe,

Thanks very much for making that macro easily accessible and including
the instructions as well. I'm sure it will benefit others.

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, NEW ZEALAND

Tel: [phone] Ext 87438
Fax: [phone]

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


-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Christophe Leterrier
Sent: Monday, 22 November 2010 10:01 p.m.
To: [hidden email]
Subject: Re: FIJI 2D stitching in a macro - solution!

Hi Jacqui,

I'm glad the macro is helpful. If someone on the list wants to re-use
it, or
for Stephan to include it, I've uploaded a fully commented version here
:

http://www.cleterrier.net/macros/Stitch_BMT.ijm

Best Regards,

Christophe

On Mon, Nov 22, 2010 at 05:52, Jacqui Ross
<[hidden email]>wrote:

> Hi Everyone,
>
>
> Christophe Leterrier has very kindly written a macro for me, which
> solved my problem. This macro tiles the 3 images together perfectly
> (even though they are a zigzag) and saves each tiled image as a
separate

> TIFF file. I was then able to open the sequence of tiled images as a
> virtual stack and save out as AVI.
>
>
>
> I have forwarded (below) the email that Christophe sent me as
> explanation of the macro. I have also included  one where I have
> described the data that I sent him, so that you will know how the
> folders work. It has taught me some useful information about how to
> write these kinds of macros.
>
>
>
> The macro is called Stitch BMT. I have copied it below. I hope the
> formatting is preserved since it wasn't last time. The macro file

itself

> was rejected by the listserver.
>
>
>
>
>
> macro "Stitch BMT" {
>
>
>
>                PARENT_PATH=getDirectory("Select a directory");
>
>
>
>                File.makeDirectory(PARENT_PATH+"tiled");
>
>                POSITION=newArray("bottom", "middle", "top");
>
>
> ALL_NAMES=getFileList(PARENT_PATH+POSITION[0]+File.separator);
>
>
>
>                for (i=1; i<=ALL_NAMES.length; i++) {
>
>
>
>
> BOTTOM_IMAGE=POSITION[0]+pad(i,3,0)+".tif";
>
>
> MIDDLE_IMAGE=POSITION[1]+pad(i,3,0)+".tif";
>
>

TOP_IMAGE=POSITION[2]+pad(i,3,0)+".tif";

>
>                                FUSED_IMAGE="fused"+pad(i,3,0)+".tif";
>
>
>
>
> BOTTOM_PATH=PARENT_PATH+POSITION[0]+File.separator+BOTTOM_IMAGE;
>
>
> MIDDLE_PATH=PARENT_PATH+POSITION[1]+File.separator+MIDDLE_IMAGE;
>
>
> TOP_PATH=PARENT_PATH+POSITION[2]+File.separator+TOP_IMAGE;
>
>
>

FUSED_PATH=PARENT_PATH+File.separator+"tiled"+File.separator+FUSED_IMAGE

> ;
>
>
>
>                                print("\n");
>
>                                print("bottom: "+BOTTOM_IMAGE);
>
>                                print("middle: "+MIDDLE_IMAGE);
>
>                                print("top: "+TOP_IMAGE);
>
>                                print("fused: "+FUSED_IMAGE);
>
>
>
>                                open(BOTTOM_PATH);
>
>                                open(MIDDLE_PATH);
>
>                                open(TOP_PATH);
>
>
>
>                                run("2D Stitching", "first_image="+
> BOTTOM_IMAGE +" use_channel_for_first=[Red, Green and Blue]
> second_image="+ MIDDLE_IMAGE +" use_channel_for_second=[Red, Green and
> Blue] use_windowing how_many_peaks=5 create_merged_image
> fusion_method=[Linear Blending] fusion=1.50 fused_image=temp.tif
> compute_overlap x=0 y=0");
>
>                                run("2D Stitching",
> "first_image=temp.tif use_channel_for_first=[Red, Green and Blue]
> second_image="+ TOP_IMAGE +" use_channel_for_second=[Red, Green and
> Blue] use_windowing how_many_peaks=5 create_merged_image
> fusion_method=[Linear Blending] fusion=1.50 fused_image="+ FUSED_IMAGE
> +" compute_overlap x=0 y=0");
>
>
>
>                                selectWindow(BOTTOM_IMAGE);
>
>                                close();
>
>                                selectWindow(MIDDLE_IMAGE);
>
>                                close();
>
>                                selectWindow(TOP_IMAGE);
>
>                                close();
>
>                                selectWindow("temp.tif");
>
>                                close();
>
>                                selectWindow(FUSED_IMAGE);
>
>                                save(FUSED_PATH);
>
>                                close();
>
>
>
>                }
>
> }
>
>
>
> function pad(number, width, character) {
>
>       number = toString(number); // force string
>
>       character = toString(character);
>
>       for (len = lengthOf(number); len < width; len++)
>
>               number = character + number;
>
>       return number;
>
> }
>
>
>
> I hope it will also be of use to others.
>
>
>
> Thanks Christophe for your efforts!
>
>
>
> 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, NEW ZEALAND
>
> Tel: [phone] Ext 87438
> Fax: [phone]
>
> http://www.fmhs.auckland.ac.nz/sms/biru/
>
> From: Christophe Leterrier [mailto:[hidden email]]
> Sent: Wednesday, 17 November 2010 10:27 p.m.
> To: Jacqui Ross
> Subject: Re: FIJI 2D stitching in a macro
>
>
>
> Hi Jaqui,
>
>
>
> The attached macro (Stitch_BTM.ijm) should run fine with the latest
> Stitching plugin from Fiji (the one with the updated fields).
>
> It runs OK on my setup for the attached folder (the same you sent me

but
> I removed the "Tiled" folder). Just run the macro, choose the
> "Christophe" folder in the dialog (you have to choose the parent
folder
> that contains the "bottom", "middle" and "top" folders), it will
create
> an additional "tiled" folder where it will store the resulting images
> with "fused00X.tif" names.
>
>
>
> One caution : the folders inside the parent folder must be named
exaclty

> "bottom", "middle" and "top", these folders must only contain images
> that are used for stitiching and no other files or images, and the
> images must be named "bottom00X.tif", "middle00X.tif", "top00X.tif"
> (with three digits).
>
>
>
> Hope this helps,
>
>
>
> Christophe
>
>
>
> On Wed, Nov 17, 2010 at 06:31, Jacqui Ross

<[hidden email]>

> wrote:
>
> Hi Christophe,
>
>
> Thanks very much for your kind offer to assist me.
>
>
>
> As you suggested,  I have attached a .zip file containing 4 folders,

3
> of which contain the raw data to be tiled. The other folder (Tiled)
> contains one merged image, which will give you an idea of the overlap,
> which is around 30%. As you will see, it's not ideal because it
doesn't
> comprise a square/rectangle, which would be better.
>
> However, the 2D Stitch plugin seemed to do this tiling effortlessly
with
> a nice result as you will see.
>
>
>
> I will look forward to hearing how you get on with this. It's not
super

> urgent so whenever you have time to take a look will be fine.
>
>
>
> 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, NEW ZEALAND
>
> Tel: [phone] Ext 87438
> Fax: [phone]
>
> http://www.fmhs.auckland.ac.nz/sms/biru/
>