Border only: border between atlas regions.Structural images: nissl and autofluorescence channels. If you want to export the atlas data in the same conditions (sampling and region), you can click Edit> ABBA - Export Atlas to ImageJ. Now the exported slices will be restricted to your user defined ROI, as shown in the gif below.Īlso, do not forget to adjust B&C once the export is done! You can click Full Size to restore the initial field of interest. You can now draw a rectangle in the region of your choice, either in review mode or in positioning mode. Most probably you will want to restore the full size before starting a registration. This region is also used to restrict registrations areas. To do this, open the Define region of interest panel, click Define interactively and draw the rectangular region of interest with the mouse. The computation for a small region can thus be much faster. You may want to export not the full slice but only a subregion of the atlas. If you choose a really too small pixel size, you may reach ImageJ’s limitation of 2 Gpixels per plane. When this process is done, you end up with an ImageJ image stack, which can be saved and handled as any other regular image in ImageJ. Processing big images will be faster by working on untransformed images in QuPath.Ĭlicking interpolate will lead to a smoother image at the cost of computation speed. It is not advised to export gigantic images this way. Usually, 20 microns per pixel gives a fast and broad overview. You can select the channels you want to export be separating them with commas, or type * to export all channels. In ABBA, select the slices you want to export, and click Export> ABBA - Export registered slices to ImageJ. Note that diminishing by 2 the pixel size will lead to a multiplication by 4 of the computation time. So try first an export with a big pixel size (40 microns for instance). If you choose a very small pixel size, be aware that the computation can take a long time. This process is also called rasterization. To export warped slices, you will need to perform a full computation of a warped image at a certain resolution - resolution that you have to choose. This allows to interactively navigate registered slices, but won’t allow for an easy analysis. So we already have warped slices on the atlas, no? In fact, the warped slices that you see in BigDataViewer cannot be used directly for analysis: only the part that needs to be displayed is warped on the fly, and at the resolution needed for a screen display. Warping slices onto the atlas Why it is not so obviousĭuring ABBA’s workflow, you observe that as you add registration steps, slices become better and better registered to the atlas (the atlas itself is sliced, but not deformed). Note that it is the fastest way to export the results (you just need to deform the outline of each region) and, because your original data is not deformed, it is also the best way to perform subsequent analysis. The point 4 corresponds to what happens in the QuPath workflow. it is possible to warp an atlas region onto the slice.it is possible to export an image of the atlas coordinates onto the slice.it is possible to warp the atlas onto a slice.it is possible to warp a slice onto the atlas.With this invertible transform in hand, the export possibilities are of many types: If the registration is not too weird, it is possible to invert this function, and thus have a way to match a pixel of a slice to its corresponding atlas coordinates. Principleīriefly, in ABBA, the registration that is stored for each slice is a function that’s capable to match a point located in the atlas to a pixel coordinates in a slice. However, other export options are available within Fiji which are explained below. For this procedure, please go to analysis in qupath. In the QuPath workflow, the atlas regions are transformed into the original slice coordinates. Probably the most useful way to use ABBA’s result is to continue the analysis in QuPath (provided that you started on QuPath). Export an image of the atlas coordinates onto the slice View the Project on GitHub BIOP/ijp-imagetoatlas Exporting ABBA’s registration results Documentation of the Aligning Big Brains & Atlases Fiji plugin.
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