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Import images

Import raw images
- Select raw images
- Enter channel names and colours for raw images
Import segmented images
Import images from multiple libraries and/or folders
Constraints on images
View image location in file system

Import raw images

To import raw images, select Files => Import… => Colour Images.

This opens the import dialog. The import dialog offers two options:

Click Add Library to select a library file, see the images it contains, then select which of the images you want to import. Library files are commonly created by microscopy software and contain a collection of images. Common examples include Leica .lif and Zeiss .lsm files.
Click Add Images to select raw image files held within a folder on your file system.

Select raw images

A file browser will appear:

Browse to the folder containing your images.
Select ics files. To select only these files, hold down the Ctrl key and click each ics file.
Click Choose.

Once you have selected the images to load, a selected images dialog will display a thumbnail and a short description of each selected image.

If you are happy with the selected images, click OK.

Enter channel names and colours for raw images

The channel names dialog will appear which allows you, for each channel in the images, to select the following:

Name: A name for the channel. Typically this will be the name of the protein strained for.
LUT: A colour scheme for the channel. LUT stands for Lookup Table which defines a range of shades for a specific colour.

When you are done, click OK.

PickCells will import your selected images and a progress bar will appear while it does so.

To open your experiment’s database folder, select Locations => Database Folder

This folder will contain one .ics and one .ids file for each imported image.

When the images have been imported, the MetaModel View will update with objects representing the images.

Import segmented images

To import images of segmentation results created using other tools, select Files => Import… => Segmented Images.

The steps to select segmented images to import are the same as already described in Select raw images.

PickCells will check that the segmented images you import have the same dimensions as the raw images you have already imported.

Import images from multiple libraries and/or folders

To import images from multiple libraries and/or folders, click Add Library or Add Images again when in the import dialog.

To view the images you have selected from a specific library or folder, click the drop-down list at the top-left of the import dialog.

Constraints on images

While there is no limit to the number of images or number of biological conditions that can be analysed in PickCells, there are a few constraints on the images you select:

Selected images must have a consistent number of channels.
Selected images can have different sizes (width, height, depth) but their resolution (voxel size) and dimensionality (2D - 3D - 4D, etc.) must be the same. To be able to compare different images, the acquisition parameters need to be consistent and so PickCells tests for this condition.
Names of selected images should be such that a pattern can be used to identify replicates and conditions (this is not mandatory, but you will find it very useful).

If any of these constraints are not met, then PickCells will notify you.

View image location in file system

You can view the location of raw and segmented images you have imported by navigating to your experiment’s database folder.