This script shows how to use the Math Operation on two sequences, with a more advanced formula.
Batch process on a folder, using a K-Means algorithm for thresholding.
Layer for 3D View that displays a Bounding Box around the object.
Deprecated: Use the Xuggler Video Importer plugin instead ! This plugin should import any kind of video.
Generate nice dataset animations with interpolated camera points.
Layer for the 3D Viewer, allowing the user to move the camera in a more intuitive way.
Used to be the micro manager libraries but now that is an empty plugin (provided for backward compatibility).
Library used by Micro-Manager for fast acquisition.
Usable on global view of a 96-Well Plates. It creates a grid of oval ROIs on the sequence and computes the mean intensity.
Removes a channel from the sequence. See also Extract Channel.
Generates various ROIs and add them to the current sequence. Shows the use of points in scripting: Point2D.
Perform a snapshot and save the result into the selected file.
Computes if a point is inside an ROI or not.
Creates a Dialog behaving like ImageJ macros'.
This script snaps an image with Micro-Manager.
Performs a threshold on the first channel of the image via the Otsu method, from BestThreshold plugin.
Example on how to use the Math Operations Plugin in scripts.
This script creates a sequence with channel 0 and a new black channel. Combined with the painting plugin, the black chan [..]
Creates a grid of 100x100 Rectangular ROIs on a sequence.
Auto Thresholder using KMeans method. Based on Thresholder plugin.
Sometimes, images metadata contains the same name, and thus are confusing for the user (two very different sequences wit [..]
Displays the value of the angles along a polyline ROI.
Save the current sequence to the file selected by the user with a File Dialog.
Displays a File Selection Dialog to choose multiple images and open them either as one or multiple sequences.
Displays a File Selection Dialog to choose an image and open it as a sequence.
Changes infos about pixel size and time interval on a sequence.
Get an image from the current sequence. Add an image, then remove it.
Get the selected ROI on the sequence.
On a sequence with multiple ROIs, get the ROI of a specified index.
Creates a sequence with 100 time points, name it, and add it to the GUI.
Creates a sequence with 100 slices.
Generates a sequence and add it to the GUI. See also "Generate Image" script.
Generates a rectangular ROI and add it to the current sequence. Shows the use of points in scripting: Point2D.
Generates a polygonal ROI (5 points) and add it to the current sequence. Shows the use of points in scripting: Point2D.
Generate an image with specified width,height, number of channels and type.
Duplicates an image, to avoid altering data.
Convert an image from a type to another.
Convert a sequence from a type to another.
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Converts sequence slices to time points.
Converts a sequence time points to slices.
Extracts channel 0 and 2 from a sequence and combine them.
Call a full macro from the script, and conversions between Icy and IJ.
Call an ImageJ Plugin from the Script.
Access pixel size and time interval on the sequence.
Access sequence width / height / channels / slices / time points.
Inversion of an ROI in python.
Extract a single channel.
A tool to parse the javadoc of a file. Mostly used now by the Script Editor.
This plugin provides a color highlighting on text. Based on RSyntaxTextArea library of Fifesoft.
Plugin Library used to provide autocompletion to JTextComponents, such as JTextArea or JTextField.
Create powerful scripts to implement what’s missing with plugins. Syntax Color and Autocomplete features implement [..]
Deprecated ! Use the new Micro-Manager blocks plugin.
This plugin allows one to use various basic sequence operations within Blocks.
Displays a scale bar overlay on the sequence. Warning: this plugin needs correct sequence metadata to be effective. Othe [..]
Display your data in real time 3D (depending on your hardware).
Tutorial on how to access single images in a video file. (Requires Icy 1.2.3)
Creates an overlay on which you can draw. This can also be used to generate specific data (for tests).
Choose the best auto thresholding technique for your data. Ported from Auto Threshold plugin in ImageJ by G. Landini (plus others, see documentation).
Record what you are doing on a sequence as a .avi file, fully compatible with Icy.
The right click on sequences and ROIs will open a menu with various features, such as image and ROI copy, data conversio [..]
A simple painter showing the current Z position in a more classy version.
Simple tool to add annotations on your images.
Edit the workspaces with a simple drag'n drop system (Requires Icy 1.2 at least).
Calibrator for Pixel Size.
Manage all calibrators for your microscope.
Advanced Acquisition plugin for microscope.
Snap complex images easily.
Move your XY Stage and Focus Device with your mouse.
Live video plugin for Micro-Manager for Icy.
Micro-Manager plugin for Icy. Use your microscope and microscopic devices in Icy ! Compatible with Micro-Manager 1.4.19 [..]
Simple chronometer for Icy.
Widget to measure distances over images considering current image scale.