[<< wikibooks] Online OsiriX Documentation/Using OsiriX Plugins/Align
WARNING! This plugin overrides a lot of fundamental OsiriX rendering routines. Many bugs are to be expected if this plugin is installed while doing anything other than creating mosaics of 8-bit images.
This plugin will make OsiriX tile images internally to increase the speed of texture uploads to the video card. This plugin has been tested using 8-bit black-on-white EM images. Some work has gone into making this plugin work with other images types. Your milage may vary. The faster texture upload speed may make this plugin useful for viewing very large images. Report bugs to Joël Spaltenstein.

= Tools for the construction of EM image mosaics by manual registration =

== Using the Align plugin ==
Open two image viewers. One will be the tile being added to the mosaic, the other is the mosaic being constructed. It may be useful to have a small white 8-bit tiff with a single pixel set to 0x00 (in order to define the dynamic range of the image) to use as the first image of the mosaic. Define the viewers as as the tile and  mosaic by using the Make Align Tile and Make Align Mosaic menu items. Now drag the file icon in the tile 's menu-bar to the mosaic, exactly as if making an image fusion. The tile should appear over the image in the mosaic window. In order to position the image correctly you will move control points on the images. Select the number of control points you wish to use with the appropriate menu items. Drag the control points in the tile to define their position. Drag the control points in the mosaic to define where the control points should map to. Once the alignment is satisfactory, make sure the mosaic viewer is the active window, and use the Merge Images menu item to paste the tile onto the mosaic. To save the mosaic, export it to a tiff, making sure of course that Set to original image size is selected in the OsiriX export preferences.

== Make Align Background ==
When creating a new mosaic, you may wish to take into account a mosaic created from EM images of a nearby slice. In order to do this, open up a viewer onto the said mosaic, Make Align Background and drag the newly created background onto the mosaic. In order to save memory, the mosaic viewer copies the image data from the background, making it safe to close the background viewer without the background disappearing from the mosaic. Of course this also means that no live link is kept between the mosaic and the background. The background can be positioned by selecting the Pan tool and panning while pressing the command (open-apple) key.

== Tips ==
Define three new CLUTs before using the plugin. One that goes from white to mostly Red and Blue, another that goes from white to mostly Red and Green, and yet another that goes from white to mostly Green and Blue. By using these newly created CLUTs, it will be very easy to see it the alignment of the new tile is good. For example, if the Red and Blue CLUT is used for the mosaic and the Green and Blue CLUT is used for the tile, the intersection of the images will appear as a sharp blue image.