Imaris Part 1: File Import using Arena

Reserve and open a ZMB image processing virtual machine.

Open Imaris

Imaris will automatically start in the new "Arena" view.

Use the "Observe Folder" icon to add folders to the "Arena" view.

It is good practice to add more than one folder to the "Observed folders" list because some views only refresh if you switch between folders.

Imaris shows you the content of the selected "observed folder" as seen in the windows file explorer.

In this section you can find the available metadata of the selected file without opening/importing the file.

The small symbols on the thumbnails indicate the file dimensions and format. The arrows indicates that a file is its source format such as .tif or .lif and has yet to be imported for visualization.

Multiple files of a series such as 3D stacks or time series are shown as a single icon with the dimensions indicated.

By Right click on a file you can open the "Configure File Series" dialog which allows to modify the dimensions of the image series for import.

For container files such as .lif which can contain multiple experiments/datasets, "Arena" shows a preview for each individual dataset.

Double click on a thumbnail for importing it into the .ims file format.

You can see the progress of your file conversion in the "Global Queues" area of your Arena view.

In order to see the effect of your import you need to refresh the file view by clicking F5 or on another folder in "Observed Folders" and then back.

Now Imaris refreshes the view and the ending of your file should have changed to .ims and the arrow is gone.

Right clicking on a file allows you to cut/copy a file or to remove it from Arena. This won't remove your file from the drive.

In the top menu you can select "Arena/Show removed items" to bring the removed files back.

You can see them now again as grey thumbnails. Right click and "Restore" on such a grey thumbnail allows you to restore it.

You can also use the "Arena" view to copy or move files between folders. This also works by drag and drop.

Double clicking on the converted file opens the "Surpass" view.

From this point on everything is the same as in the old versions of Imaris.

In the data folders of your "Observed Folders" you will find a new folder called ".imaris_cache". Here Imaris saves the thumbnails and some metadata.

By generating this cache, Imaris does not need to index the "Observed Folders" each time you access it. Which speeds things up quite a bit.

Deleting this folder does not do any harm besides forcing Imaris to re-index the folder which takes some time.