In confocal imaging we get many stacks of images which can be reconstructed in a 3D format.but most imaging analysis takes into account a 2D projection of all the frames, which makes our analysis faulty (because many cells would upregulate and yet may not be visible because it is in some other frames). So my strategy is to do pixel based analysis across all the frames, determine which regions get up-regulated and then construct the 2D projection.
To sum up I'm attaching my idea in a picture.. I need help in creating a the pseudocode for my problem
•
written
by
murmublog •
3 answers
I feel like there should be some sort of plug-in for ImageJ/Fiji, but I haven't done this particular analysis before. This is what I found with a quick Google search:
http://imagej.1557.x6.nabble.com/2D-image-to-3D-in-ImageJ-or-Fiji-td5000113.html
If you need to automate the process, you can write ImageJ macros:
•
written
by
Charles Warden
Hello,
Try seeing SD cube image rail, if this has been implemented here, you might get code for it as they have released API
•
written
by
abhay.krishna •
You can try to use opencv for this kind of analysis: http://opencv.org/ it is available in C++, python, java.
but I fear that the code is going to be too specific for your problem to get any general help here.
Log in to answer this question.
-
GSEA analysis
written by Ahmed •
-
3d plot in matplotlib of my own data
written by Eli •
-
VisCello Shiny app code for hosting snRNA-seq data
written by LacquerHed •
-
Converting REFSeq IDs to Entrez IDs for KEGG analysis - "geneid of incorrect length"?
written by saw44 •
-
Does sample size matter when calculating linkage disequilibrium using RAD-Seq loci?
written by j.mcintyre.1 •
-
Outliers in microarray dataset - Possible explanation?
written by User43533445 •
-
1000Genome SV integrated map's power for SV filter
written by michealsmith
-
Cell-type-specific RNA-Seq using genetic ablation
written by drosophiliac •
-
Need Help Understanding Spliced Sequence Alignment Algorithm
written by corn8bit •
-
Gene Expression Network Analysis
written by shalinisonar •
"I have discovered a truly marvellous proof of this, which this margin is too narrow to contain"
Hi Pierre can u elaborate me bit more?So that I can truly appreciate what u are saying
Pierre was being a bit snarky :)
Isn't there an imageJ plugin that does something like this? If so, try to see if you can find its code.
Well, my experiment will be like this. My steps:
So suggest me an pseudo code as I'm new to coding not much idea...so I need a way to start.
I'm not seeing an image? (Unless it's on on dropbox, perhaps, and blocked by the proxy here?)