Imaris Part 1: File conversion and opening files

Reserve and open a ZMB image processing virtual machine.

Open ImarisFileConverter.

Either Drag & Drop the files you wish to convert, or click "Add Files...".

If you have *.lif (Leica) files containing 2D and 3D you might be asked to change the voxel size.

Imaris 9.9 is not able to handle LIF files with mixed 2D and 3D datasets.

If your files have different z step sizes this change will affect all your files!

You can hoover over your file name to check the dimensions of the different datasets.

Until this bug is fixed please use the workaround of doing the conversion in Imaris Arena.

It is recommend that you save your processed files in a different folder than your raw data.

Click "Specific Folder:".

Choose the desired folder path.

Multiple files of a series such as 3D stacks, time series and multi channel images should be automatically recognized as a single *.ims file.

If the dimensions are not properly detected you can select your file and click on "Settings".

Here you can adjust the dimensions of the image series for conversion.

In the example each file correspond to a different channel (C). The same principle would apply to different Z planes (Z) or timepoints (T).

For container files such as .lif (which can contain multiple images/datasets) an individual *.ims file for each image/dataset will be generated.

You can now start converting your files by pressing "Start All".

If the conversion is successful you will now see a green mark next to your files.

Open your specified folder and double click to visualize your file.

Alternatively you can also use the Arena view in Imaris to browse through the different files. Please check the corresponding guide.