Grid Stitch Tile Configuration file

stitching
imagej

#1

Hello,

I’m using the Grid/Collection Stitching Plugin and am running it as Positions from file, Defined by TileConfiguration. Starts running just fine and then throws error looking for a file after the last file in the folder. Seems like I did something wrong with my TileConfiguration.txt.

I followed the template provided on https://imagej.net/Image_Stitching#Problems.2C_known_issues_and_solutions:

# 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)

To review, if img_78.tif is the last, I’m getting an error of can’t find img_79.tif
Any suggestions?


#2

Hi @Snowotarski,

From what you described, my first thought is that maybe you have
an empty line at the end of your text file.

John


#3

Hi, could you please post the actual error and the log, this would help I think. Thanks a lot, Stephan


#4

… and your complete tileconfiguration file as well as a screenshot how you run the plugin, thanks!


#5

Hi Stephan,

Thank you so much for your response.

The initial problem was solved by John above. But now I am getting a Java “ArrayIndexOutOfBoundsException :2” once the log in displays “Fuse & Display”. Any idea on that?

You can see screenshots of my set up running the plugin. The forum doesn’t want me to upload.txt files so I also made screenshots of the last view of the log as well as the relevant portion of the exception.

Thanks!
Steph

END OF LOG

!

exception|690x482


#6

exception here


#7

You got it, thanks!

I’m now running into a java ArrayIndexOutOfBoundsException :2
I’ve asked Stephan Preibisch about it below.

Any ideas on that?

Thanks again!
Steph


#8

Are your tiles 2d or 3d?


#9

tiles are 2d. this question makes me think that I’m setting my z position wrong in the (x,y,z) part of the file maybe?


#10

@Snowotarski

Yea, @StephanPreibisch will know for sure, but
I’d try changing to dim =2
and omitting the z-coordinate in your tile configuration file.

Good luck,
John