Contents
- Description
- How Composite .gif files are created during experiment loading
- Replacement of .gif files in SMD
- Note
Related Help Documents
- Experiment Entry: Explanation on how to enter hybridizations (arrays) into the Stanford Microarray Database.
- Normalization: This document describes the normalization procedures available in the database.
This text describes how to replace an image file representing an array in SMD. This replacement may be necessary if the image does not look satisfactory after it was created by the default process during loading of the experiment. Another reason may be a renormalization of the data, after which you might want this change to be reflected on the image of the array. You can replace the image of an array in SMD, by following the Upload gif link on our Search & Analyze page.
The two image files (.tif files) resulting from scanning an array slide are too large to easily store or retrieve quickly. To reduce their size, the .tif files are used to create a much smaller composite image that is stored as a .gif file and used for display purposes every time an image of the whole array or a spot on the array is needed online. The original .tif files are archived, backed up to tape and are not easily accessed thereafter.
Several steps are involved in creating a composite image. Using the same normalization factor used to adjust the data, the intensity of every pixel in the channel 2 (red) .tif file is adjusted. After this, the two image files are overlaid, colored red and green, and combined. The resulting file is adjusted for maximal contrast, saved as a .gif file and used any time an image of the array is needed by programs in SMD.
Because of the way this .gif file is created it may not look the best visually and it may look very different from the image you saw during scanning. If you wish, you can replace the image in the database with another one that represents the slide better.
Once you decided to replace the array image in the database make a new composite image from your own copy of the original .tif files. For this purpose, you can use any imaging program that can save the resulting image in .gif format (use eg. Photoshop). When ready, ftp the resulting file into the incoming/ directory of your loader account.
To replace the previous image in SMD, follow the Upload gif link on our Search & Analyze page. Make sure you use the correct slide name that corresponds to the image you want to replace. Enter the name of the .gif file at the end of the path: /incoming/image.gif and hit the Upload gif button.
Renormalizations following the initial normalization done during experiment uploading will not affect the image file of the array in the database.