imagejextension v0.3.1

ImageJExtension

This is an electrongui extension. This is an extension for electrongui.

It uses ImageJ tool for performing some of the available image processing tasks (see ImageJ documentation for better understanding how this extension deals with this tool).

Authors

• Gherardo Varando gherardo.varando@gmail.com
• Mario Juez mario@mjuez.com

Requirements

To avoid license problem and to distribute a slimmer extension, we decided to not distribute Imagej with the extension anymore. ImageJ need to be installed in the system (see https://imagej.nih.gov/ij/) and the ImageJ extension need to be configured. It is also possible to install ImageJ from the ImageJExtension.

ImageJ is written in Java and needs Java Runtine Environment (JRE) installed in the system to work. In order to avoid possible performance issues (memory issues), installed JRE version must match with the operating system architecture (32bit / 64bit).

User guide

This extension adds a submenu to the application menu called "ImageJ". Six main tasks can be done:

1. Launch ImageJ

ImageJ user interface can be launched through "Launch ImageJ" menu entry. This tool can be useful for performing some preprocessing operations to prepare images for Atlas usage.

2. Configure ImageJ

ImageJ JVM memory settings (heap and stack) can be configured. By default, Java heap memory is set to 70% of total system memory, and Java stack memory is set to 515MB.

3. Map Tools

Map Tools is a toolbox for creating Atlas maps. This toolbox is an ImageJ plugin that requires an image or folder with images and the following parameters as input:

• Map name (default: "map").
• Pixel tiles dimension (default: 256).
• Maximum zoom (default: 5).
• Use all slice (default: no): if source image has more than one slice and this option is checked, a map for every slice will be created.
• Merge all slices (default: no): if source image has more than one slice and this option is checked, a max intensity projection (ImageJ ZProjection) of all slices will be performed and the output will be used as input for map creation.
• Slice used (default: 1): if source image has more than one slice, this option allows to choose what slice will be used as input for map creation.
• Output folder: the path where output map will be saved.

With this toolbox, creating layers is also possible. The difference between a map and a layer is that a map contains a JSON configuration file with information about author, map name, and the different layers that make up the map. A map created with this tool will have only one layer. Adding new layers must be done modifying configuration file manually.

3.1. Map/Layer creation from image

When using this option, a dialog will be opened to choose source image, then previously defined parameters can be configured. When this task finishes, the map can be added to the workspace, or the layer can be added to a map in the workspace.

3.2. Map/Layer creation from folder

This option is intended to create a map (or layer) from a big image which is splitted in a small collection of images. Each image name must contain its X and Y coordinates in the big image. For example, partial_image_X0_Y0.tiff will be the image in the left upper corner.

When using this option, a dialog will be opened to choose the left upper corner image, then Atlas needs to combine all images and the user will be asked to configure previously defined parameters and three additional image combination parameters:

• Initial slice (default: 1).
• Last slice (default: 1).
• Scale (default: 1.000): the combined image scale, this parameter goes from 0 to 1 (original size).

When this task finishes, the map can be added to the workspace, or the layer can be added to a map in the workspace.

4. Object Detection

Object detection is a tool for detecting objects in an image. For this purpose, obj_detection ImageJ plugin is used, which calculates object centroids using image segmentation techniques. This extension allows to detect objects from a single image, from a folder with many images, or from a list of images, In all cases, following parameters can be configured:

• Minimum radius (default: 1): MaxLoGs Min R parameter.
• Maximum radius (default: 5): MaxLoGs Max R parameter.
• By (default: 1): MaxLoGs step parameter.
• Threshold method (default: "Moments").
• Minimum (default: 1).
• Maximum (default: -1).
• Fraction (default: 0.500).
• Tolerance (default: 0).
• Output folder: the path where detected objects data will be saved, usually the folder with the map of the image being processed is used.

When this task finishes, the layer with detected objects data (called points layer) can be added to a map in the workspace.

5. Holes Detection

Holes detection is a tool for detecting holes in an image. For this purpose, obj_detection ImageJ plugin is used, which calculates holes using median filtering and thresholding. This extension allows to detect holes from a single image, from a folder with many images, or from a list of images, In all cases, following parameters can be configured:

• Radius of median filter (default: 10).
• Threshold (default: 250).
• Output folder: the path where detected holes data will be saved, usually the folder with the map of the image being processed is used.

When this task finishes, the layer with detected holes data (called pixels layer) can be added to a map in the workspace.

6. Mosaic creation

This tool is located inside "Tools" submenu, it allows to divide a big image into small parts (tiles). The following parameters must be configured:

• Tile size (default: 10): Defines the width and height of the output tiles.
• Original image height (default: 10).
• Original image width (default: 10).
• X0 (default: 0): The start number for generated tiles in X axis.
• Y0 (default: 0): The start number for generated tiles in Y axis.
• Output folder: the path where splitted parts (tiles) will be saved.

Each tile name will be the original image name plus its X and Y position, e.g. original_image_X0_Y0.tif usually will be the upper left corner tile.

License

The MIT License (MIT)

Copyright (c) 2017 Mario Juez (mjuez@fi.upm.es), Gherardo Varando (gherardo.varando@gmail.com)

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.