multireg 0.0.0

Registration of 3D multiplex images with one common chanel

multireg

Registration of 3D multiplex images with one common chanel

The stacks must have one common chanel (typically cell junctions and nuclei) that is used to calculate the registration transformation. It can be rotated, translated, deformed, and with a wider field of view. Then the calculated transformation is applied to all the other chanels for each stack. The final result is a multi-chanel 3D stack.

The common chanel can be averaged between the different chanels, which improves its quality.

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Installation

You can install multireg via pip:

pip install multireg

Usage

You can launch multireg in napari by going to Plugins>multireg: do multiplex registration.

Fixed image

It will open a prompt to ask you to select the reference (fixed) image, compared to which all other images will be aligned. Then you have to choose the reference chanel that will be used in all the stacks to calculate the alignement. So this chanel should be common to all stacks.

Reference points

The first part of the registration relies on reference points manually selected, because the common field of view can be quite far from each other in the acquisition. So first a affine registration is applied to bring close the region of interest between the two stacks to match.

You have to manually placed a few reference points (4-5 should be enough). Try to spread them in the image (in x,y and z) on landmarks to recognize them in other images.

To add a new reference point, click on the "plus" sign in the left panel. To select one, click on the arrow icon (or press 3), then on the point. You can move the point in x and y. To move it in z, press 'u' for up and 'd' for down. When all points are placed, save them.

Moving image

Then you can choose one of the images you want to align with the reference image.

License

Distributed under the terms of the BSD-3 license, "multireg" is free and open source software

Plugin initialization

This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.

Issues

If you encounter any problems, please [file an issue] along with a detailed description.