Posted by
María Antonieta Sánchez Farrán on
Sep 17, 2015; 6:42pm
URL: http://imagej.273.s1.nabble.com/GridCollection-Stitching-question-tp5014355.html
Hello,
I am a new Fiji user and I would like to get your help. I've tried
different things before posting but I am not sure if I am using the right
tools for my purpose:
- I am running a simulation, with an output consisting of a total of *N*
2D-grids (png images). Each grid has 29x40 cells (and each cell has 40x40
pixels). I have *N*~1000 grids because they capture the time evolution of
the system.
- The cell color reflects the "state" of a cell, with two states (and hence
colors) allowed. Grid generation is done by a script, so I control the
colors. For example, each cell is either blue or red.
- I would like to use time as the z dimension and stack the *N* grids. The
generated volume would allow me to visualize the evolution of the system
(if a cell is in the same state all the time, I should just see a long
"rod" expanding throughout the entire z dimension).
This is what I've tried so far:
1. Tried the GridCollection/Stitching plugin > Row by row > Right Down but
I am not sure how the variation in z axis is captured. I see that the grid
size z option appears in a deprecated version of the plugin.
2. I cropped all cells and labeled them as
image-Z_{iii}_Y_{iii}_X_{iii}.png and selected GridCollection/Stitching
plugin > Positions from file. For testing purposes, in the grid
configuration script I only consider the first two z values. I am not sure
what options to select in the window. I enabled "Compute overlaps" and
"Display Fusion" but it appeared the
"java.lang.ArrayIndexOutOfBoundsException".
What is the most convenient approach to complete this task?
Thank you for your time,
Maria
--
ImageJ mailing list:
http://imagej.nih.gov/ij/list.html