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Script List

Current number of scripts: 81

Access sequence width / height / channels / slices / time points.
Access pixel size and time interval on the sequence.
Adds a black channel to an existing sequence
This script creates a sequence with channel 0 and a new black channel. Combined with the painting plugin, the ...
This script will convert each sequence in a .lei/.lif file in individual Tif file. Convert sequences are reco...
This script shows how to resolve an Ambiguous error raised by JavaScript.
Displays the value of the angles along a polyline ROI.
Auto Thresholder using KMeans method. Based on Thresholder plugin.
Performs a threshold on the first channel of the image via the Otsu method, from BestThreshold plugin.

Batch process on a folder, using a K-Means algorithm for thresholding.
Use the Spot Detector and Spot Tracking plugin in a batch way (multiple movies directly loaded from a local lo...

Call a full macro from the script, and conversions between Icy and IJ.
Call an ImageJ Plugin from the Script.
Extracts channel 0 and 2 from a sequence and combine them.
Converts the image type
This script converts the ROIs of the active Sequence in a set of detection (DetectionResults) and export it in...
Converts a sequence time points to slices.
Converts sequence slices to time points.
Convert a sequence from a type to another.
Convert an image from a type to another.
This script takes the current active sequence and loop over its region of interest. For each ROI, it displa...
Creates a Dialog behaving like ImageJ macros'.
This protocol will iterate through all ROIs from the active Sequence and create for each ROI a new fixed size ...
Crop a sequence and copy the source ROI in the cropped sequence.
Crops a sequence.

This scripts takes a time-sequence as input. Then it use the spot detector for each image separately, using a...
This script is a modification of the script "Detect spot and change parameter along time" but it is using batc...
Detection script with post processing: box around mass center of each detection and display a ROI. Computes th...
Performs detection using WAT computation for each ROI independently. Practically, the script saves all the ROI...
Duplicates an image, to avoid altering data.

Simple example using loop roi and excel output
This script compute and exports the mean intensity and the standard deviation for a complete folder of image i...
Extract a single channel.
This script shows how to create a graphical user interface in Python, using the EzPlug SDK. Writing an Icy ...

Generate an image with specified width,height, number of channels and type.
Generates a polygonal ROI (5 points) and add it to the current sequence. Shows the use of points in scripting:...
Generate a random colormap for the current active image.
Generates a rectangular ROI and add it to the current sequence. Shows the use of points in scripting: Point2D.
Generates various ROIs and add them to the current sequence. Shows the use of points in scripting: Point2D.
Generates a sequence and add it to the GUI. See also "Generate Image" script.
Creates a sequence with 100 time points, name it, and add it to the GUI.
Creates a sequence with 100 slices.
On a sequence with multiple ROIs, get the ROI of a specified index.
Get the selected ROI on the sequence.

Get an image from the current sequence. Add an image, then remove it.
Inversion of an ROI in python.

JMath Plot script

Performs a binary threshold using KMeans on an image smoothened with a Gaussian filter (kernel 3x3). Similar ...

This script shows how to use the Math Operation on two sequences, with a more advanced formula.
Example on how to use the Math Operations Plugin in scripts.
This script, measures the Mean Intensity in each ROIs in a GrayScale. you Must Open a picture file, select yo...
This script asks the user for an experiment folder produced by Axiovision and will create a multi-channel tiff...
Take an input folder containing several XLS files and merge them together while adding a new column containing...
This script take ROI(s) from an input image and create cropped image(s) from it / them then continuously acqui...
This java script show how to perform a timelaps (20 frames) and Z-Stack acquisition trough Micro-Manager and a...
This simple example show how to perform a single image acquisition with Micro-Manager for Icy from the java sc...
This java script show how to perform a small Z-Stack acquisition trough Micro-Manager. WARNING: You need to...
Changes infos about pixel size and time interval on a sequence.
Move all selected ROIs together

Displays a File Selection Dialog to choose an image and open it as a sequence.
Displays a File Selection Dialog to choose multiple images and open them either as one or multiple sequences.
Usable on global view of a 96-Well Plates. It creates a grid of oval ROIs on the sequence and computes the mea...

This script allow you to export all pixels values which are contained in the ROI(s) into a excel file.
This script allow you to export all pixels values which are contained in ROI(s) into a excel file. Process is...
Computes if a point is inside an ROI or not.

Removes a channel from the sequence. See also Extract Channel.
Rename all ROIs of the active sequence
Sometimes, images metadata contains the same name, and thus are confusing for the user (two very different seq...
This script exports the ROI infos to an excel file. Here we just show it as an example for min, mean and max i...
Creates a grid of 100x100 Rectangular ROIs on a sequence.
Export the min / mean / max intensity of the selected ROI of active sequence over time in an excel file. The ...
This small script export all contained pixel (position and value) into a CSV file. Warning: this script may...
Convert ROI(s) to labeled image. This script basically iterate over all the ROIs of the current active image ...

Save the current sequence to the file selected by the user with a File Dialog.
Here is what this script does from an input image: - apply a gaussian filter to improve the segmentation -...
This script snaps an image with Micro-Manager.
Perform a snapshot and save the result into the selected file.
A small script to synchronize all LUT (color map and histogram) all of opened images from the current active v...

for test purposes only

Shows the different manners to create and access an Array in JavaScript.

This script illustrates how to adjust (some of) the camera parameters in a 3D VTK viewer