18.1. Scans and images

18.1.1. Scan properties
18.1.2. Images

When you have done your hybridization and scanned it, you can register information about the scanning process as a Scan item in BASE. A scan item holds information about the scanning process, such as which scanner and what settings you have used. It can also hold information about the images that was produced as well as the actual image files.

[Note] Note
A scan does not have information about the spots or raw data. The process of analysing the images is considered a separate step. This information is held by raw bioassays.

18.1.1. Scan properties

A scan has the following properties:


The name of the scan.


The hybridization this scan comes from.


The scanner that was used (optional).


The protocol used for scanning (optional). Scanning parameters may be registered as part of the protocol.


A decription of the scan (optional).

A scan can have annotations. Read more about this in Chapter 11, Annotations.

18.1.2. Images

If you want you can upload the images from the scan to BASE. This is optional, but the images are needed if you want to create spot images later on.

To upload images for a scan you must first go to the single-item view for the scan. On this page you will find the Images tab which will take you to a list view of the images from this scan. New images are created in the same way as any other item in BASE, by clicking the New… button. You may add as many images as you like.

An image has the following properties:


The name of the image. The name is automatically generated from the name of the scan, but you may enter a different name.


The file containing the actual image data (optional). Use the Select button to select an existing file or upload a new one.


The image format (optional). You can select between TIFF, JPEG and Unknown.


If the image is a preview image or the full scan.


A description of the image (optional).