GridCollection/Stitching question

[María Antonieta Sánchez Farrán]

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

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[Majurski, Michael Paul (Fed)]

Maria,

First key question: do your images overlap? I am not sure that I fully understand how your images are arranged.

As for visualizing the resulting time series you can load it into Fiji and view it as a stack of images, letting you flip back and forth through time.  Once you have the images loaded as a stack you can also use the "Plugins > 3D viewer" to render a volume which you can then manipulate. In addition, you might want to try "Plugins > Volume Viewer" as it might do what you are looking for.

To setup the Grid/Collection stitching plugin it sounds like you want to select "Filename defined position" because you have images where the filename contains the images position in the grid. For example, "Z_{ii}_Y_{ii}_X_{ii}.png" where " Y_{ii}_X_{ii}" defines the images grid position relative to the other images be specify its x and y index. For example, "Z_01_Y_01_X_01.png" should be the first image in the upper left hand corner. "Z_01_Y_01_X_02.png" should be the second image in the first row of images. If that is how your data is laid out, and there is overlapping content between images the Grid/Collection Stitching plugin should be able to produce a result for you.

One thing to be careful of, the Grid/Collection stitching plugin requires "File names for tiles" to follow this sort of pattern "Z_{zz}_Y_{yy}_X_{xx}.png" when using filename defined positions. In addition, if you define the Z, I believe the plugin will try to register the images as a volume, computing displacements along the Z direction as well. If this is not what you want then you will most likely have to set up a script to iteratively call the stitching plugin. Since, as far as I am aware, there is no functionality built into the Grid/Collection stitching plugin to iteratively stitch a time series of images.

As for the checkbox options in the Grid/Collection stitching plugin, I only ever use the "compute overlap" and select "Write to Disk" as the "Image output". I leave everything else as default.

If your images form a regular overlapping grid (all the overlaps are almost equal) then I can also point you to my stitching tool for which I am much more knowledgeable about the inner workings. It also can handle stitching a time series of images as a single job.

MIST source code:
https://github.com/NIST-ISG/MIST
Wiki:
https://github.com/NIST-ISG/MIST/wiki
Installation Instructions:
https://github.com/NIST-ISG/MIST/wiki/Install-Guide

Thanks,
Michael Majurski






-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of María Antonieta Sánchez Farrán
Sent: Thursday, September 17, 2015 2:42 PM
To: [hidden email]
Subject: GridCollection/Stitching question

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

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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