3D Drift Correction

[Tamlyn Peel]

Hi

Currently moving all my workflow to Icy so I can automate most of my analysis and reduce my reliance on different programmes (Volocity, Imaris, etc). I'm generating 5D images of T cells in lymph nodes using two photon microscopy; currently I use Volocity to do my initial 3D drift correction based on fluorescence from YFP-DCs as it works well and can be batch processed, but I think the only option for this in Icy at the minute is Rigid Registration, which only does 2D (X-Y) drift and needs a reference slice, which is going to get upset with Z drift. There's a plugin for FIJI called Correct 3D Drift (http://imagej.net/Correct_3D_drift) which seems to do the same job as Volocity, but as it's FIJI I can't call it from Icy. That's available as a Python script, but I guess it's not a simple case of drag and drop into Icy.

Is there any way to implement this in Icy, or any plans for 3D drift correction? Or have I missed an existing plug in that can be made to work?

I can most things to work well in Icy, and loving the protocols to build batch processing tools quickly without having to code.

Cheers

Tamlyn