Automated

The 3D Rotation plug-in allows you to record a 360 degree rotation of the current focused 3D VTK viewer about the vertical screen axis.

The 'angle step' parameter indicates the deviation in degrees between two consecutive snapshots. Increasing the angle will increase rotation speed (up to a point where it might look like jumping more than rotating) and reduce the final movie length.

JRuby script that will take an image stack and generate from it an image that should appear in 3D when viewed through red and cyan glasses. All that this does is to do two maximum intensity projections from two slightly different angles and merges them together.

The purpose of this plugin is to create a text file with a list of files from Gatan’s 3View montage image stacks. This text file can then be used to automatically import all the images into TrakEM2, as they are, stored in the original directories.

This plugin can find the smallest bounding box of an image (or a rectangular part defined by a selection) by cropping as much background as possible. Found in Fiji, under Image> Adjust.

In the version labeled with (guess background color), the plugin tries to determine the background color by looking at the pixels on the border of the image, while Auto Crop uses the currently selected background color which can be changed by double-clicking on the pipette symbol or using the Image > Color > Color Picker....

Instead of cropping right away, you can set the selection to the rectangle that would be cropped to using Edit > Selection > Select Bounding Box.