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© 2002-2007 by
Chih Long Liu

Bliss Filename Nomenclature

The TMA data management system described here was designed with the Bliss filename nomenclature in mind. If you created and curate your digital image collection with the Bliss microscope system, your files will already be in this format. If you have not, the following will describe how the nomenclature is structured so that you can adapt your system appropriately.

Images generated by the Bliss microscope system (Bacus Labs Inc.) are stored in the following directory structure:


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for a larger view

All TMA directories should be contained in the directory "Composites", as shown above. Each directory or folder represents a collection of images from a single sector of a given slice of the TMA, as shown above. The total number of folders in the selection will equal the product of the number of arrays, slices, and sectors in your TMA collection. In the example above, which also represents the files stored in the on-line demonstration database, there are 8 folders, representing an array composed of 4 slices and 2 sectors each.

The directory name is composed of the following:

C-TA-0x-0y.z.Ab-Name

An example of this would be the following:

C-TA-04-02.34.bcl2

where:

Variable Description Example
x TMA Array Number 4
y TMA Sector 2
z TMA Slice Number 34
Ab-Name Antibody Name bcl2

So, in the above example, the folder/directory represents images collected from TMA number 4, sector 2, slice 34, stained with the antibody against bcl2.

Each of the image filenames in these directories consist of the following:

s_a_c_r_sl_code_d.jpg

An example of this would be the following:

1_4_1_1_34_1012_1.jpg

where:

Variable Description Example
s Sector Number 1
a Array Number 4
c Column Number 1
r Row Number 1
sl Slice Number* 34
code Bliss Code Number* 1012
d Order Number 1
* Note that the raw scoring workbooks used to generate the TMA TreeView files must contain the necessary information in order for Stainfinder to recognize the filenames. This is why the TMA Deconvoluter will warn the user if "Bliss or slice information" is missing from their scoring worksheets.

So, in the above example, the folder/directory represents image collected from Sector 1, Array 4, Column 1, Row 1, Slice 34, Bliss Code designation 1012, and is the first picture scanned in the array.

A note about the Bliss code numbers: The BLISS code number is a numerical code for the name of the antibody used in staining and is required since the name of a JPG image file generated by the Bliss system consists of 7 numbers separated by underscores, but does not allow for letters.

Your digital image collection must follow this nomenclature in order for Stainfinder to work properly. If there are missing or incorrect information, Stainfinder may not be able to retrieve the image file or may retrieve incorrect image files. Please examine the on-line demonstration database and accompanying files from the Downloads section to see how a properly configured system should behave.

Note: The Bliss microscope system employs a serpentine scanning method in generating the order of pictures collected. The Order Numbers reflect this scanning method. An example of a serpentine scan is shown below, where the numbers represent the order in which the images are acquired.

Serpentine Scan

Sector n Column
Row 1 2 3 4 5 6 7 8 9 10 11
1 1 2 3 4 5 6 7 8 9 10 11
2 22 21 20 19 18 17 16 15 14 13 12
3 23 24 25 26 27 28 29 30 31 32 33
etc....

Scanning beings at Row 1, Column 1 of Sector n and proceeds to the end of the row. It then moves one row down and proceeds to the left, until it reaches the left end of the row. It continues onto the third row and proceeds in like fashion until the end of the sector is reached.

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Last edited by Chih Long Liu on January 17, 2007