![]() ![]() Tick the box next to the one you want to open and press OK. This second window displays all of the experiments in a list. When opening files with multiple experiments, a second window will be displayed after the opening options. These can be opened separately through bio-formats importer. Some files will contain multiple image stacks or experiments within one file. Specific planes, channels or time points can also be extracted when working with stacks (discussed in section 8), but in some circumstances, opening separately can be a quicker or easier option to use. All images will open, but you can easily close the ones you don’t need. This can be useful if you want to extract a single z-plane or time point from a series, or only want to display one channel from your image. Selecting the boxes next to split channels, focal planes or time points will result in each plane opening as in individual image, rather than a stack or hyperstack. The file will open with the assigned colours. In the resulting Bio-Formats Custom Colourization window you can set the RGB colour values for each of the channels. You can do this in Bio-Formats Importer by selecting Custom from the drop down menu under Colour Mode. Sometimes colours can’t be assigned correctly from the metadata or you may want to assign specific colours to your image. Here you will find information including things like bitdepth, channel information, acquisition parameters and scale. Metadata will be displayed in a separate window to the image as a list. ![]() Then click OK to open both the image and metadata. To view the in-built image information, known as metadata, select the box next to Display Metadata in the options window of bio-formats importer. These different options and variations in opening files with the Bio-Formats Importer are discussed below followed by how these variations apply to common file formats. When you have selected all options you want, click OK to open the image. In the options window you can change the settings for metadata, separating channels, z-planes or time points into single image windows and colour options. With the Bio-Formats plugin installed, you can also open most compatible file types by going to File -> Open and selecting your file, or dragging and dropping onto the FIJI interface as you would any other image file.ĭuring the opening process for all file formats the Import Options window will open, unless you have previously set ‘windowless’ opening for that file type under configurations. You can import files by going to Plugins -> Bio-Formats -> Bio-Formats Importer. You can come back to configurations and reverse this if you need to change import options at another time. This speeds up opening but means you cannot change import settings on individual images and all images will open with the default settings (or those previously set by you when opening files with Bio-Formats). Selecting the Windowless box will open these file formats without first opening the import options window. Select your file format from the list to check it is enabled and see compatible extensions. Select the Formats tab from the top to display and modify the available programs and equipment. To do this go to Plugins -> Bio-Formats -> Bio-Formats Plugin Configurations. You can check the file types enabled in the Bio-Formats importer, as well as turn specific formats on and off and change preferences by opening the configuration settings. It is also known as LOCI tools, this is the plugin name for ImageJ.Įxamples of the different file types discussed in this section (Leica, Olympus, Nikon, DeltaVision, Zeiss) can be found in the Bio-Formats folder of demonstration images. This is a pre-bundled plugin in FIJI but it must be downloaded separately for ImageJ. However, these formats can be easily opened in FIJI using the Bio-Formats Importer. Images saved in raw file format from microscope software packages are unique to that software and often will not open in standard image viewing software. ![]()
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