Comments (9)
Hi @tcdoe, can you please post screenshots of the GUI that you use? It could be that you are maybe selecting the wrong options ...
from stitching.
shure,
here's one where I just use the xx and yy
https://i.imgur.com/8xejydZ.png
and then one with zz, yy, xx.
https://i.imgur.com/lRyXkoi.png
funny thing is that i've done this before and had it working no prob, that was a couple years ago.
from stitching.
of course, the files are there. I tried putting them into a generic C:\test folder and same error.
from stitching.
Hi @tcdoe, you select the wrong mode (Grid: row-by-row: Right & Down). You need to select "Positions from file" instead, you can this described in detail in the documentation (https://imagej.net/plugins/image-stitching#grid-collection-stitching). Then {xx} and {yy} will work.
Best,
Stephan
from stitching.
Hi, Thanks very much for reply! but that doesn't seem to work quite as you describe.
If I use Positions from File, or Filename defined Position, and put in:
{xx} and {yy}, the Filename defined position works for 2D, e.g. only for {xx} and {yy}, but not for {zz}.
I get the same file not found error.
I will continue to try different variations of the TileConfiguration.txt file
Do I really have to hand-make a custom TileConfiguration.txt file to get this to work in 3D?
It seems extremely tedious, and nothing in the documentation indicates that. But if I have to, no problem it will at least be good to know that that is the only way.
I get this working good for 2 dimensions, but dim=3 hasn't worked so far.
Define the number of dimensions we are working on
dim = 2
Define the image coordinates
testneur3d10x_L01_R01_C01.jpg; ; (0.0, 0.0)
testneur3d10x_L01_R01_C02.jpg; ; (2406.0, 0.0)
testneur3d10x_L01_R01_C03.jpg; ; (4812.0, 0.0)
testneur3d10x_L01_R02_C01.jpg; ; (0.0, 2400.0)
testneur3d10x_L01_R02_C02.jpg; ; (2406.0, 2400.0)
testneur3d10x_L01_R02_C03.jpg; ; (4812.0, 2400.0)
testneur3d10x_L01_R03_C01.jpg; ; (0.0, 4800.0)
testneur3d10x_L01_R03_C02.jpg; ; (2406.0, 4800.0)
testneur3d10x_L01_R03_C03.jpg; ; (4812.0, 4800.0)
from stitching.
Hi, for dim=3 you usually use 3D images (e.g. a 3D TIFF) and not slices ... maybe that is the problem?
from stitching.
Hi Thanks, I just have separate images in tiles; each image is a jpg.
So you can think of it as what I thought it would be a simple extension of 2D image "tiles", eg: testscan_Z{zz}_Y{yy}_X{xx}.jpg
But I think now I understand that I would have to build the Z levels into such as a 3D TIFF for each X-Y 'tile', and then 'stich' those together in bulk.
Again, thanks very much for your help. I guess I'll try the above, and see what I can get.
I've made a 3D scanning microscope; so now I'm trying to generate simple volumetric images from XYZ scanned tiles.
I'm probably looking at this a bit too simplistically.
Best!
from stitching.
Hi, as a first step I'd resave them to a 3D Tiff using Fiji and try if it actually works ... that is straight forward. Extending Stitching is always possible, but somebody needs to do it :)
from stitching.
Thanks will do. Fortunately I got the 3D Tiff to generate, still working on the rest. Boosting my memory to 128G hope that's enough :))
from stitching.
Related Issues (20)
- Printing Stitching Parameters in "Results" instead of "Log"?
- "java.lang.ArrayIndexOutOfBoundsException: 2" for Positions from file .... an .ome.tiff - specific issue HOT 1
- FEATURE REQUEST: increase the limit on the length of file names HOT 9
- Stitch of Z-stack of
- stitch of Z-stack of more than one channels
- Leica LIF files not getting their coordinates in the right place
- Grid/Collection stitching plugin output doesn't always match what's written to registered.txt
- Calibration in saved stitched images is lost HOT 1
- "Sequential images" breaks if the sequence reaches over 99 images HOT 1
- Ignoring Z-tile movement in stitching doesn't work HOT 3
- Error while building from source: Plugin or class not found
- ROI Picker install HOT 1
- Missing a scrollbar at the "Confirm files" window ! HOT 1
- Unable to Read Subfolders
- Exception in thread "main" while run the source
- Dependency org.yaml:snakeyaml, leading to CVE problem
- Can stitch without blending? HOT 2
- Stitching .tif files ends in a all white image HOT 2
- Saving unreasonably slowly in headless HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from stitching.