8 ImageJ
ImageJ is a free open source image processing software. It has an open architecture that allows you to extend the processing and scripts available. In this section we will be looking at some of the OMERO tools available to work with ImageJ. OMERO has made two plugins for ImageJ. The OMERO/ImageJ plugin and the Bio-formats plugin both are available to download.
To begin all we need to do is to start ImageJ by double clicking on the ImageJ icon.
8.1 OMERO/ImageJ Plugin
8.1.1 Reading an Image from OMERO
Once ImageJ has been launched the ImageJ main interface will appear as shown below.
To access the OMERO plugin, click on Plugins -> OMERO -> Import from OMERO as shown below.
Selecting this menu entry will bring up the OMERO login page as shown below.
Using your username and password provided, login to the OMERO system. This will present the project/dataset/image hierarchy view as shown below.
Using this hierarchy view it is possible to expand projects and datasets to navigate to an image. Double clicking on an image will load the image from the OMERO server into ImageJ into the 5D viewer as shown below:
- Open ImageJ and run the OMERO plugin
- Login to the OMERO server
- Navigate to an image by expanding the hierarchy view
- Double click on an image to view it in ImageJ
The various dimensions of the image can be navigated using the provided sliders.
Exercise 2:- Open a multi-channel image in ImageJ from OMERO
Once an image is loaded into ImageJ it is possible to use all process/analyze/plugin options in ImageJ.
Exercise 3:- Try despeckling an image by running Process->Noise->Despeckle
8.2 Bioformats Plugin
The Bio-formats plugin allows you to use the bio-formats library as is used by OMERO.importer to read over 100 image file formats, as well as save these formats to OME-TIFF/XML. To use the bio-formats plugin from ImageJ we will launch ImageJ to bring up the main interface as shown below.
8.2.1 Reading Images using Bio-formats
To read one of the formats supported by bio-formats we will access the plugin, by clicking on Plugins -> LOCI -> Bio-formats Importer as shown below.
This will bring up a dialogue box as shown below allowing you to load an image into ImageJ.
After an image has been selected the load options will appear. This will allow you to choose various options upon import.
The most useful options are the ability to view the original and translated OME metadata. The ability to use a virtual stack for images that are too big to fit into memory as well as the dataset organisation options allowing you to group/swap/concatenate dimensions and files. Note that upon mouse over of any of the import option information is displayed at the bottom of the dialogue box.
So data formats allow for multiple image series to be present within a file. The bio-format plugin can automatically detect if this is the case and if an image series is present will prompt you with the following dialogue to let you pick the images of interest.
If any metadata option have been selected for the import, these will appear as separate windows as shown below:
The default view for an image is to display it as a hyperstack, which will present the image as shown below:
Exercise 4:
- Launch the Bio-formats importer by selecting it in Plugins->LOCI->Bio-Formats Importer
- Select an image to load from the Sample Data folder found on the desktop
- Select both original and OME-XML metadata viewing
- Navigate the image dimensions using the hyperstack sliders
- Apply a despekle process to the image
8.2.2 Writing an Image to OME-TIFF
Any image loaded into ImageJ can be exported to OME-TIFF, by selecting Plugins->Loci->Bio-Formats Exporter. This will then bring up a file dialogue box asking you for a location and filename to save the file to. Using this options allows you to save your microscopy images to an open TIFF compatible file format. This is particularly useful to facilitate working with analysis software.
