Opening Proprietary Data Sets

Introduction

Fiji, through use of the LOCI (Laboratory for Optical and Computational Instrumentation) tools plugin Bio-Formats can open a large range of image formats. Over recent years this ability has been steadily improved to a point where pretty much any microscope format can be easily opened using this plugin. 

The following example uses a Leica LIF file but the steps and outcomes are essentially the same for any other proprietary format.

Bio-Formats

Initial File Opening

When a file is opened Bio-Formats will detect if it can open it or not and present you with the following dialog.

You can get information about each of the options by hovering the mouse pointer over it, a description will appear in the information box to the right. 

In the top left is a drop down menu that lets you select how you want to view the stack. In general HyperStack is the best choice if you want to be able to easily create 3D views, make movies and change channel colours. Image5D has the same functionality with a few extra features that tend to complicate things more than they make it easy.

Displaying Metadata

In most cases a large amount of data about the image capture is stored in the files metadata. This includes information about the type of microscope used, calibration values, laser powers etc. To display this data you can either tick the Display Metadata box when opening a file or (if you only want to see the meatadata and not the image) select Metadata Only from the View stack with: pull down menu.

Default Opening States 

Once you have decided on a standard way of opening a given file format you can set LOCI to open it the same way every time without giving you the import dialog window.

1. Go to Plugins 🡪 LOCI Tools 🡪 LOCI Plugins Configuration

2. In the resulting dialog window there is a list of image formats that LOCI can open on the left hand side. By selecting the desired format (In this example AIM) and checking the Windowless box LOCI will open the image directly without showing the import box. 

Opening Confocal Data Example

Leica – LIF Format

Leica confocal data (.lif files) usually contains multiple image stacks or experiments within one file. Nikons ND2 file format and some other manufacturers save data in this way. Others will save data as a single file per stack, timepoint or position. 

1. Open Leica.lif found in Demo Images\Confocal. The LOCI import window will open. Select to view the data with Hyperstack, make sure all other boxes except for the autoscale box are unticked and press OK.

NOTE: If you have a large dataset and a computer with a small amount of RAM ticking the Use Virtual Memory box will only load in the files/slices/time points etc. as they are needed, instead of loading the whole stack into memory. This will however perform slower and certain plugins and filters may not work with a virtual stack.

2. You will then see a window that has thumbnails representing the different data sets contained within the file. Tick the box next to the one you want to open and press OK. 

NOTE: Ticking multiple boxes will open all the ticked data sets. This could lead to memory and stability issues.

3. The resulting hyperstack should contain all the channel, z and time information from the selected data set. In this example there is only 3 channels with no Z, stage or time data. These would appear as additional slides at the bottom (Z for depth, a triangle for time and a S for position)