make montage from series of stacks

[kurt_]

Dear Community,

I have 36 stacks (folders) of images where each folder represents a z-stack from a 6x6 montage of SBF-SEM images. In other words, a large area was mosaic imaged in 36 images, all files from the first plane were named layer_000 and saved into the appropriate one of 36 stack folders to annotate its x-y position. Thus, a file named layer_008 in each of the 36 stack folders must be stitched together to make a montage of z=8. Then ideally all of these large mosaics would be registered/aligned in the z-direction.

Is there a plugin created with this structure of data in mind? If not, would it be best to start with assembling all the images from one plane into a mosaic and then creating a stack of those large mosaics and registering these images? Any advice on this assembly process would be greatly appreciated.

Regards,
Kurt

[Pariksheet Nanda]

On Fri, Mar 1, 2013 at 6:45 PM, kurt_ <[hidden email]> wrote:
> ideally all of these large mosaics would be registered/aligned in the z-direction.
>

You may not need to worry about this.  The Z movement precision will
likely be fine if the images were collected with a piezo or linear
encoded Z device.


> Is there a plugin created with this structure of data in mind?
>

Yes, use the Grid/Collection stitching plugin
(http://fly.mpi-cbg.de/~preibisch/).  In FIJI this is under Plugins >
Stitching > Grid/Collection

Since each slice of the x-y positions are stored in a separate folders
you may need probably to move (and possibly rename) all the images
into a single folder, but perhaps you might not need to do that and
could set the "File names for tiles" to include the stack folder name
when running the plugin.

If you have a lot of data you could run the write a small macro to
call the plugin.  The recorder is useful to see which variables you
need to override
http://fiji.sc/Introduction_into_Macro_Programming#The_recorder

To stitch the first plane without a macro, for file names you could
use "my folder name {ii}/layer_001".  If you write a macro you could
use a variable for the layer number.


> Kurt

Pariksheet

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[ngdias]

I picked up this thread now while searching in Google for something else. Maybe it's too late be of help, but it sounds like what you're looking for is the TrackEM2 plugin in FIJI's flavour of ImageJ's.

http://fiji.sc/TrakEM2

Let me know if you need help with importing the files.

Nuno Dias.