http://imagej.273.s1.nabble.com/FIJI-2D-stitching-in-a-macro-solution-tp3686366p3686369.html
> 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: 64 9 373 7599 Ext 87438
>> Fax: 64 9 373 7484
>>
>>
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: 64 9 373 7599 Ext 87438
>> Fax: 64 9 373 7484
>>
>>
http://www.fmhs.auckland.ac.nz/sms/biru/>>
>