3D Template Registration via natverse

[Emine Ozen]

Hello,

I am very new to natverse and I am hoping to use it for template registration of my 3D panneuronally labeled whole brain images of Drosophila. I am confused as to how to get started. I see there are the packages nat.flybrains and nat.templatebrains that could be potentially useful, but are there any written instructions on how to actually use the functions and templates there? Thank you so much.

All the best,

Emine

[Greg Jefferis]

Hello Emine,

Thanks for your interest in the natverse. Perhaps you could try to define your goal a little more precisely and we can try to help with suggestions for examples/documentation.

Best wishes,

Greg Jefferis.

[Greg Jefferis]

Dear Emine, Thanks for the additional information. Registering a calcium indicator dataset is a bit more complicated as you need both to align the within-fly dataset over time as well as align across flies where the anatomical template brains will have higher resolution imaging with a different microscope and .

I suggest that you take a look at this paper from Tom Clandinin's group which uses many of the same tools (I gave some early stage input) and covers the process nicely:

https://doi.org/10.1016/j.cub.2017.06.076

They include 3 separate alignments

1. Within fly

2. Within imaging modality across fly

3. Across imaging modality to anatomical template brain

Which I think is required to optimise the final alignment.

The natverse packages that you highlighted allow you to map pre-aligned data between different template brains and also provide some assistance if you have eg segmented neurons or meshes in one dataset to which you wish to apply a series of registrations to map into another space. But this is a downstream problem in your analysis pipeline.

With best wishes,

Greg.

On 6 Feb 2023, at 16:59, Emine Ozen <eo2...@columbia.edu> wrote:

Hello,

Thank you for your response. I have datasets of 3D whole brain imaging of Drosophila adults over time labeled with a panneuronal calcium indicator. I would like to register my datasets to a template brain, such as JFRC2, to identify the anatomical structures in my datasets. If there is any, a walk through example for registering a dataset to one of the template brains in the literature would be very helpful.

All the best,

Emine