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Bug 332 - Stitching plugin fails on 16-bit zvi files
Stitching plugin fails on 16-bit zvi files
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
Macintosh Mac OS
: P2 normal
Assigned To: Stephan Preibisch
Depends on:
Blocks:
 
Reported: 2011-06-30 17:46 CDT by Jan Eglinger
Modified: 2012-05-12 06:31 CDT
0 users

See Also:
Description Jan Eglinger 2011-06-30 17:46:50 CDT 
Several issues related to Stitching Zeiss .zvi files:

When I run the command "Stitch Multiple Series or Tile Scan File" on a zvi file containing a 3x3 mosaic, 2channel, 16-bit image, the image gets opened as RGB and the pixel intensity data gets messed up. It looks like pixel value above 255 get mapped to (values modulo 256).

In addition, when using "Compute overlap", only 4 tiles of a 9-tile image I tried to open actually were displayed (although there was significant intensity and structure in the missing tiles as well).

On the other side, if compute_overlap is unchecked, the 3x3 image opens correctly (although unstitched, just roughly montaged), but with black space of about 20 tile widths to the right of the image.

I'll try to upload a sample image to illustrate the issues.

Cheers,
Jan
Comment 1 Jan Eglinger 2011-06-30 18:02:56 CDT 
I've uploaded a sample image to

http://fiji.sc/wiki/index.php?title=Special:Incoming&dir=%2Fvar%2Fwww%2Fuploads%2Fincoming%2Fmosaic3x3.zvi

(don't be surprised if you open it, it's oversaturated in one channel and almost black on the other, but it reflects relatively well some of the more difficult use cases we have in the lab..)

These are the commands I used to open the file:

- To open it without computing any overlap:

run("Stitch Multiple Series or Tile Scan File", "file=[path_to_file] increase_overlap=0 fusion_method=None fusion=1.50 regression=0.30 max/avg=2.50 absolute=3.50");

- To stitch it together "nicely":

run("Stitch Multiple Series or Tile Scan File", "file=[path_to_file] compute_overlap increase_overlap=10 fusion_method=[Linear Blending] fusion=1.50 regression=0.30 max/avg=2.50 absolute=3.50");

Hope that helps to clarify the problem.
Jan
Comment 2 Johannes Schindelin 2012-01-06 00:01:49 CST 
I recall that Stephan worked on this. Is this resolved now?
Comment 3 Johannes Schindelin 2012-05-12 06:31:16 CDT 
I guess it is.