How to make many microscopies alignment (X, Y, Z), containing multiple stacks, permanent?


I’m currently working with 3-dimensional reconstruction of neurons using .tiff microscopies containing multiple stacks. Some of the neurons are split into many microscopies containing diverse slice numbers and superpositions (as shown in the sketch). Using Neuromantic software, I’m able to align the images (X and Y) AND stacks (Z) position manually, but it takes a long time, too much work and I can’t save the process, every time I open the image set I have to realign.

My question is, how can I make the aligned mosaic permanent? Is it possible to maybe manually align all the images just once and then save it as a new, single .tiff image?

Example sketch (colors represent different microscopies/.tiff images and numbers its slice quantities):

Thanks in advance and best regards!

Hi @Ket,

Welcome to the forum.

I’m not familiar with Neuromantic, so can’t give you specific advice about it.

Fiji has some tools that do what you need automatically / semi-manually. I recommend that you try Bigstitcher, which is definitely capable of what you need, and might actually save you time if it can do the alignment automatically.

Good luck

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