How to align images sequence from a time-lapse microscopy experiment (multi-channels)

I have images from a time-lapse microscopy experiment (multiple channels and multiple time points). Unfortunately, due to microscope drift the consecutive time points are not exactly at the same XY position (slight systematic shifts between time points).

  1. I would like to use the align function to iterate over all time points and sequentially re-align this shift.
  2. Since this I have images from multiple channels, I would like to use only one channel (the one with tagged nuclei) to calculate the drift and then propagate the shift and crop values to other channels.

Could this be done with the align function or any other module?


PS - I’ve been using CellProfiler for a almost a month and am finding it extremely useful (thanks for the great work)

Hi Amir,

In the Align module you can click on “Add another image”, which then can be shifted according to the drift computed between the first two images. However, I don’t know how you apply the Align function to a time-lapse as you would have to somehow drift-correct subsequent time-frames…but other people in the forum might know this!

I just wanted to point out that if you download the latest Fiji and use [Plugins>Registration>Correct 3D Drift] you can register a multi-color time-series (2D or 3D) in one go. You can chose which channel should be used for computing the drift. You can even put a ROI on the image to select a region that should be used for computing the drift.

Cheers, Christian

I’m not sure of a CP way to do this either but I’ll look into it; I use the FIJI plugin MultiStackReg which while it doesn’t come built in works really well for me.

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Thanks Christin - FIJI is a good option (although I was hoping to have an intact analysis pipeline only in CP). I wasn’t aware of the specific plugin you mention - sound like exactly what I need.

Thanks Beth - If you can find a way to do it in CP it will be very useful.

Has anyone used CellProfiler’s Align for time-lapse registration in the release CP 3.1.9? This Github issue implies that it might work now?

I’m Grouping the time-lapse images, but in Align I don’t see any way to specify a time-lapse movie/stack, i.e. it just shows “first” and “second” image inputs. And if I choose the same for first and second, the output shows that there is no X/Y shift, implying that there is really no alignment being performed.
@bcimini @agoodman

That issue to me looks like it was closed as a “wontsolve”, sadly. I’m pretty sure that was never implemented.

I like StackReg/MultiStackReg in FIJI for that, FWIW.

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