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Microscopy Image Browser - New Arena for Imaris 9.3 | Tutorial

New Imaris Arena is designed to act as a multifunctional image browser for microscopists.

To add a Drive or a folder to Arena, simply Select an “Observe folder” icon which scans a selected folder or a drive and adds it to Arena. Imaris mirrors the structure of your folder or drive and provides an immediate view of data thumbnails.

While Imaris is visualizing thumbnails for the first time, behind the scenes it creates an additional Imaris Cache folder which contains the information allowing even faster thumbnail preview when opening forlder in Imaris Arena for the next time.

In the new Imaris Arena  you can observe both: internal or external drives or network locations.

A very useful function is the smart thumbnail creation, so that tiff stacks are represented as single thumbnails - not individual images as in internet explorer. Also multi-image files (such as lifs) are represented as individual thumbnails for each dataset. This function allows you to quickly browse the content of their drives and folders even if the files are stored in native formats.

In addition you can quickly preview the properties of your dataset without opening the file. Properties, such as dimensions, size, channels or description are visible in the Arena panel on the right. Moreover, when you have worked with your datasets in Imaris before, you can see the image processing operations and detected objects.

From Imaris 9.3,  Imaris File Converter is integrated in Arena. If you see a “conversion” symbol on the bottom of the thumbnail, it means that the file is not saved in the ims file format yet. Right click on the thumbnail and select “Convert to native Imaris file format”. This action triggers Imaris File Converter which runs in the background. You can see the progress of your conversions in the right panel. When the job is finished, the conversion symbol disappears from the thumbnail and you can see a stack of two thumbnails. Double left clicking on the thumbnail opens the Imaris file, nevertheless both files: original and Imaris are stored in the same folder. You can see both files in the Internet Explorer.

Conversion can be run in parallel for multiple files. Please note, that the converted file is saved into the same folder as the original file and it’s not possible to change the output path from Arena. If your files are too big and don’t fit into the input folder or you need to specify different locations for converted files, please use Free Imaris File Converter Stand Alone Application prior to working with Imaris.

It is important to know that Imaris Arena not only mirrors your file folder structure but also allows copying or deleting files from the drive.

If you want to move a selected file to a new destination, simply drag the selected thumbnails holding left-mouse button and drop it to the new location within the left panel showing the folder structure, You can also right click on the thumbnail and “Copy” or “Cut” the file and then “Paste” it into the new location within Arena. All operations are immediately reflected on your drive

To delete files you need right click  on the thumbnail and select “Remove from Arena” from the menu. If you want to remove a group of files at once, simply select multiple files with Shift+Left click or select multiple files with left mouse button. In this step you can only remove selected files from Arena but they are not deleted from the drive yet.

In order to show removed files, go to the Arena menu within the top ribbon and select: “Show removed Items” or use the Ctrl+H shortcut. The Items which were previously removed from Arena have greyed out thumbnails. Right click on them to see the options. Now you can either “Restore” selected items to Arena or “Delete from Disk”. We implemented this two-step option to prevent users from accidentally deleting important files from their drives.

Doing Clean ups, back-ups of your drives, or copying selected files to the new locations was never easier.

Category: Tutorial

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