Part of the Oxford Instruments Group

Importing Data into Imaris

The very first step to open a file in Imaris is to convert it into IMS format. To do so, we can either use Arena directly, or, if you want to convert files in batch, we can use the standalone File Converter.

First let's look at Arena. Here I have an image containing tiff files. For files that are not in ims format, you will see the arrow icon, indicating that the file needs to be converted. Simply double click on the image, and the conversion will automatically start. Once the conversion is done, Arena will only show the ims format, and hide the original file. You can still access the original file by going to the folder directly.

If you have multiple files that need to be converted, or if you need to change certain settings of the image dimension, File Converter may be an easier way to batch this process. Either click ‘Add Files’, or drag and drop the files to convert.

If you have tiff series, File Converter automatically groups the files with the same file name, and use certain delimiters as the guide to recognize the image dimension. Here I have the tiff series named ‘Celldemo’, which has 3 colors and 18 Z slices. Dragging any one of the tif files into FileConverter, and it will pick up all 54 files with the same name. We can check the dimension it recognizes from ‘Settings’. With proper delimiters like ‘_C’ and ‘_Z’, FileConverter should pick up the dimension correctly.

Click ‘Start All’ to run. Please make sure you have enough hard drive space before converting large files. 

Sometimes the files may not come with proper delimiters. In this folder, I have the same Celldemo files but without _C and _Z as delimiters like in the previous example. When we load the files into FileCovnerter, it still picks up all the files, but when we check in ‘Settings’, we can see that it’s mistaken 3 channels as 3 time points.

We can change it to ‘C’ so it will save it as ‘Channel’ and output the same result as before. Alternatively, we can select ‘F (split)’ to save these 3 channels as separate ims files. Let’s try this option. As you can see, three new ims files are generated, and each contains one channel, with 18 z slices.

Date: Sep-20

Category: Tutorial

Download as pdf


Related assets