Hi,

I am trying to reformat a volumetric time series recording (GCaMP fluorescence). I have produced a 3D stack of the Maximum Intensity Projections of the time series of each plane and recorded this to a reference brain. I now need to apply reformatting to the whole 4D dataset so I can analyze cell activity in the reference space. Is this possible?
Thanks!!

Francesco

Torsten may know if there is a cleverer way to do this, but one simple option is to generate 3D stacks for each timepoint and then apply the registration to each of them. This is how munger handles 4D (3D + colour) multichannel stacks. If you had provided the following stacks in your images/ folder

stack01.nrrd - time averaged sample stack
stack02.nrrd - timepoint 1
stack03.nrrd - timepoint 2
…

Then munger would handle this automatically if you pass in options

-r "010203"

I'm sure you could also script something this for your own data fairly easily.

As an alternative, if your analysis requires some kind of mask in reference space, have you considered moving that into the sample space? You would do a lot less reformatting.

Best,

Greg.

Originally posted by Greg Jefferis:


Hi Greg,

right on!!! That's exactly what I needed!!


Thanks!!!

Francesco