#UCI IMAGEJ SOFTWARE UPDATE#
#UCI IMAGEJ SOFTWARE SOFTWARE#

You can select two default parameters - region thickness and size. By default, there are processed all region types. You can also specify which region types should be processed. First, you should select a directory with segmented images. Region AnalysisĪfter marking organelles on a set of images, it is possible to measure a group of parameters on them. You can select the brush size, the precision of the graph cut and smoothness, which enhances the result of graphcut method. The tool can be also adjusted using parameters. * Right mouse click - adds a background marker * Left mouse click - adds a foreground marker The segmentation is driven using initial foreground and background markers. When using the tool all previously marked regions of the same type are removed. The tool cannot be combined with other tools. The primary usage is to separate a cell from the rest of the image. The graphcut tool can be effectively used to separate a large segment from background.

#UCI IMAGEJ SOFTWARE UPDATE#

Update region parameters - region size and smoothness Graph Cut Select one point located in a region of interestĢ. After the initial region growing, the region is smoothed using geodesic active contours method.ġ. The region grows faster on flat regions and slower on edges. The region grows from the seed point to its neighbourhood according to a local intensity change. A selected region is inicialized using a seed point. The region growing tool is convenient for fast seleciton of cell parts which have an oval shape.

Double click - Finishes selection and creates a new segment (user points can be still edited).

Right mouse click - removes the last user defined point.

Left mouse click - adds a new point through which the path goes.

The path goes more likely through points with higher intensity change (edges). The tool finds a path between user defined points. Every slice contains all regions of the same type. The created regions are stored into image as new slices. To do that, choose selection tool, select a part of an image and click on Add Selection or Remove Selection button.Įvery change of processed image which is done using this form is reversible. You can also modify segmented regions using standard selection tools which are in the ImageJ toolbox. The form offers two semiautomatic segmentation tools (described further) and eraser. To add or modify particular segment of a cell you can use the following form which is accesible from image viewer. To open the tools use the button Edit Regions. The region types (organelles or other cell structures) can be edited in the file config.txt (see Plugin Configuration).Įvery image can be edited using semiautomatic segmentation tools. You can show the lables and the region names. Different regions of the same type are distinguished using labels. If the images are segmented already, you can display particular cell parts. The option allows to go through all images from one directory.

It garantees that image calibration is kept. For image opening, it is used the Bio-formats plugin.

When using our plugin it is recomanded to use the plugin option Open Images. The standard way to open images in ImageJ is through the File->Open. Masks of detected cell and nucleus are stored into output image as two new image slices. In such a case, it is appropriate to convert input images to lower resolution using preprocessing. Posslibly, there can be parts of other cells. The tool requires single cell with single nucleus in every input image. provides an automatic tool for segmentation of cell and nucleus. The real image scale is recalculated according to change of image resolution. The preprocessing preserves image calibration. To keep the original data, you should set a different output directory. you can convert images to lower resolution or change their bit depth. – calculates a group of parameters on images from a given folder – opens a window for browsing images and organelle segmentation detects cell and nucleus on every image in a given folder and exports a segmented image to another folder preprocesses images in a given folder (image size, bit depth) and exports them to another folder

There is a list of tools with a short description:

There is an example of an input image:Įvery plugin tool is accesible from the main menu in Plugins->TEM Images. The plugin is designed to process transmission electron microscopy images.

#UCI IMAGEJ SOFTWARE SOFTWARE#

The software has been developed in terms of project MUNI/M/1050/2013 and supporded by Grant Agency of Masaryk University. The plugin also supports automatic cell and nucleus segmentation. It contains semiautomatic tools for segmentation of organelles and allows their analysis. It is implemented as a plugin for ImageJ (image processing and analysis program). This software is designed to process transmission electron microscopy images containing cells.

Uci imagej software