Bug 695 – BioFormats Stitch Tiles Option does not work correctly for CZI Datasets

Bug 695 - BioFormats Stitch Tiles Option does not work correctly for CZI Datasets


Summary:	BioFormats Stitch Tiles Option does not work correctly for CZI Datasets

Status:	RESOLVED FIXED

Product:	Fiji
Classification:	Unclassified
Component:	Bio-Formats
Version:	unspecified
Hardware:	PC Windows

Importance:	P5 normal
Assigned To:	ImageJ Bugs Mailing List

URL:

Depends on:
Blocks:

Reported:	2014-01-21 02:27 CST by Sebastian Rhode
Modified:	2014-07-01 10:17 CDT
CC List:	1 user (show)

See Also:

Attachments
Screeshot with the result from Stitch Tiles (509.35 KB, image/png) 2014-01-21 02:29 CST, Sebastian Rhode

Description Sebastian Rhode 2014-01-21 02:27:43 CST

Hi,

I just tested BioFormats with the Stitch Tiles Options (Fiji is up-to-date) and found a problem. The tile image is a 2x3 Tile with 96 Z-Planes.
But the shown result is a 3x3 tile

--> see screenshot = BioFormats_Stitch_Tiles_Problem.png

It contains some empty tiles.

Nervertheless, when I try to really stitch that data with the stitching plugin, everything works ok. So I assume, that in principle the stage coordinates & Co are OK.

From a short look, the OME-XML data shown from the BioFormats import look OK to me...

The data can be found here:

https://dl.dropboxusercontent.com/u/623476/406-ZFOK-SD-T%3D2x3_Z%3D96_CH%3D1.czi

Comment 1 Sebastian Rhode 2014-01-21 02:29:13 CST

Created attachment 129
Screeshot with the result from Stitch Tiles

Comment 2 Curtis Rueden 2014-06-26 22:29:17 CDT

Sebastian, with the recent fixes to the CZI format inside Bio-Formats, does this problem still occur? If not, can you please close the issue as fixed? Thanks!

Comment 3 Sebastian Rhode 2014-07-01 10:17:26 CDT

Just tested it. Works fine now.