These are chat archives for fiji/fiji

22nd
Mar 2017
shavi1995
@shavi1995
Mar 22 2017 14:08
Hello! I have a fluorescent set of images taken at x20 over 3 channels accounting for 600 odd images - I wonder if anyone knew of a way to stitch them using image j ?
I've got the metadata file for it too -unfortunately - when i run it on the grid/collection plug in it reads unknown format exception/ unknown file formate
*even though my file format is .xml
I've tried googling extensively, and am knew to imagej and have nil knowledge of java and any help would be greatly appreciated! thanks
John Bogovic
@bogovicj
Mar 22 2017 14:11
@shavi1995 , is this the plugin you tried? https://imagej.net/Image_Stitching
shavi1995
@shavi1995
Mar 22 2017 14:12
yes - the grid/collection stitching plug in is the one
John Bogovic
@bogovicj
Mar 22 2017 14:16
Probably the plugin does not understand how to get the meta data out of the xml
(It sounds like you gave that to the plugin right?)
Choosing the "positions from file" option? is that right?
shavi1995
@shavi1995
Mar 22 2017 14:18
yes that's right
can image j read any .xml meta data file or does it need to be in a particular format?
John Bogovic
@bogovicj
Mar 22 2017 14:19
It has to be in a particular format, its described on that page i linked above about 3/4 of the way down
it looks like:
# Define the number of dimensions we are working on
dim = 3
# Define the image coordinates (in pixels)
img_73.tif; ; (0.0, 0.0, 0.0)
img_74.tif; ; (409.0, 0.0, 0.0)
img_75.tif; ; (0.0, 409.0, 0.0)
img_76.tif; ; (409.0, 409.0, 0.0)
img_77.tif; ; (0.0, 818.0, 0.0)
img_78.tif; ; (409.0, 818.0, 0.0)
If you need help getting your xml to this format, post something on the forum, and I or someone else can try to help
shavi1995
@shavi1995
Mar 22 2017 14:21
oh! i thought that was just for the tile configuration.txt but is this true for the metadata file too?
John Bogovic
@bogovicj
Mar 22 2017 14:22
err, ya, I thought the "tileConfig" is what you meant by metadata...
is there some other metadata?
shavi1995
@shavi1995
Mar 22 2017 14:23
That's the metadata file I was given - how would i get it into this format?
John Bogovic
@bogovicj
Mar 22 2017 14:24
ah, ya that file looks to have the information that would go into the tileConfiguration file
shavi1995
@shavi1995
Mar 22 2017 14:24
okay perfect!
John Bogovic
@bogovicj
Mar 22 2017 14:25
you'll need a script to convert it to the format above. I recommend you point to that xml on the fo
*on the forum
and I or someone there can help
shavi1995
@shavi1995
Mar 22 2017 14:30
okay - I have just posted thanks!
John Bogovic
@bogovicj
Mar 22 2017 14:30
:+1:
Curtis Rueden
@ctrueden
Mar 22 2017 15:16
@shavi1995 If you have an XML metadata file which was written by a particular microscopy software, then it might be supported by Bio-Formats. The Stitching plugin leans on Bio-Formats to convert proprietary file formats (PFFs) into a standard which can be consumed by plugins like Stitching.
You would have to share a sample non-working dataset for us to comment further. Best is to write to the ImageJ Forum: http://forum.imagej.net/
For completeness, the aforementioned new thread is, I think, this one.
John Bogovic
@bogovicj
Mar 22 2017 15:36
ooo, that would be great, thanks @ctrueden
tpietzsch
@tpietzsch
Mar 22 2017 21:58
updating poms to parent pom-scijava makes me so angry
sometimes somebody needs to explain to me what all the bureaucracy is good for...
i have no license and no contributors and yes sure mailing list is the imagej forum why not
I just want to get on with my life
:worried: