clij - GPU-acceleration for ImageJ

Description

clij is an ImageJ/Fiji plugin allowing you to run GPU-accelerated code from within Fijis script editor (e.g. macro and jython). CLIJ is based on ClearCLImglib2 and SciJava. It contains components for image filtering, thresholding, spatial transforms, projections, binary image processing and basic signal measurements.

CellProfiler Crop

Description

Crop crops or masks an image.

This module crops images into a rectangle, ellipse, an arbitrary shape provided by you, the shape of object(s) identified by an Identify module, or a shape created using a previous Crop module in the pipeline.

has function
need a thumbnail

Crop 5D

Description

Select a portion of a sequence in all 5 dimensions.

has function

ICY Context Menu

Description

ICY plugin,

the right click on sequences and ROIs will open a menu with various features, such as image and ROI copy, data conversion and extraction. See documentation for more information.

has function
need a thumbnail

ImageJ Auto Crop

Description

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.

has function

KNIME Auto Crop

Description

Automatically crops an image by finding the smallest bounding box which still contains all pixels of the specified value.

Options include Pixel values, Margin, and more...

This KNIME node is included in the KNIME Image Processing Extension

has function