[Up - The Gel Parameter Dialog]

Gel parameters

Each parameter is listed with its descriptive name (as used in the project defaults dialog and the gel parameter dialog) and its keyword name in quotes (as used in the data-file). The keyword name is also used for identifying parameters for the built-in configurations. If a parameter has a fixed range of values these are listed with their descriptive name (as used in the option-menu in the dialog windows) and their keyword-value name in quotes (as used in the data-file).

The data-files mentioned here refer to either the project defaults file or the gelinfo-file. The project defaults are written to <projectdirectory>/.projectrc, the gelinfo-file is written to <geldirectory>/info. These two directories are shown above the project chooser and the gel chooser in the Image startup window.

gel type
"geltype"
Describes the method that was originally used to produce the gel image.
Value range:
Autoradiogram
"ARG" - autoradiographs derived from restriction digest fingerprinting
ABI
"ABI" - fluorescent fingerprinting on ABI machines
Fluor Imager
"FLI" - agarose gels scanned on the FluorImager system
lane number
"lanenumber"
Total number of lanes on the gel including marker lanes. For multi-dye ABI gels this varies greatly from the number of clones that have been loaded on the gel. Enter the total number of lanes per dye.
Value range: Integer numbers between 1 and 1000.
marker repeat
"markerrepeat"
Describes the interval at which marker lanes are loaded on the gel. The intervals have to be evenly spaced across the gel, otherwise the resulting gel-image is unsuitable for processing with the Image software.
Count the number of sample lanes between two markers and add 1.
Value range:
0
if no marker are used on the gel (only useful for testing)
1
if every lane is a marker lane, only possible on multi-dye ABI gels.
2-1000
lanes from one marker to next
Note: - Adjust the lane number and marker repeat values such that (lane number - 1) divided by the marker repeat leaves no remainder.
zone number
"zonenumber"
Parameter for the lanetracking. If you think of the lane-grid (see Step 2) as lines connecting the teeth of a set of combs, this parameter is the number of combs.
Using a big number will cope better with curvature of lanes, but this will leave much more grid points that may have to be edited if the lanetracker goes wrong.
Value range: Integer numbers between 1 and 100. A number less than 10 is usually enough for gels with very straight lanes. Use 15 or more for gels with bendy lanes.
dye number
"dyenumber"
Only meaningful in case of multiplexed ABI gels, otherwise 1.
Value range:
4
for ABI gels
1
for all other types.
component order
"componentorder"
Only used in case of multiplexed ABI gels, otherwise ignored. You may wish to view the dyes in a different order from the standard (B,G,Y,R). For example, if your markers are loaded in the red channel, then this would be 4 1 2 3.
Value range: Four integers between 1 and 4 separated by spaces (comma separated in data-file). Each of the number 1, 2, 3 and 4 must be present, even if the dye number is 1. In that case this parameter is not used anyway.
digest order
"digestorder"
Only used for single channel digest gels (ABI excluded). This parameter is used when the names are first initialized for the gel. As well as a clone name per lane, those gels also carry a digest name per clone. As the digests are often repeated all across the gel, this cyclical order can be set here.
If you are using digests, you may have alternated the digests SauIIIa and HindIII across the gel. Enter the text SauIIIa:HindIII in this field and the colon separated fields of the text will be cyclically repeated in the digest name fields (visible in Step 3.
Value range:
blank
if digest names are imported from an external clone names utility or if they will be edited by hand, a blank value is recommended.
"-"
if the digest names feature are not used on this gel at all, please enter a dash (or hyphen) in the field.
<d1>:<d2> etc..
i.e. colon separated text fields as explained above.
standard file
"standardfile"
Complete pathname of standard file.
The [...] button let's you select the file using the file chooser.
Value range: This has to be an absolute pathname beginning with a / (on a UNIX system).
gel training file
"geltrainingfile"
Note: BSTT is no longer supported for Image Version 3.10 and above anymore.
If you have used BSTT from previuos releases to train the gel analysis in the past, enter the name of the training file here. If you have training data for this project it is most likely to be stored in the file <projectdirectory>/.geltraining.
The [...] button let's you select the file using the file chooser.
Value range: leave blank or enter the absolute pathname beginning with a / (on a UNIX system).
naming scheme
"namingscheme"
Parameter used when the clone names are initialized. Ignore this parameter if your setup imports the clone names from an external utility.
In order to guess the initial clone names you can specify the first clone name, and the program then fills in all other names based on the first name and the naming scheme. If the clones are numbered by their plate position it is probably desirable to use the last two character of the first clone name, e.g. A1 to guess the others from that : A2, A3 ... A12, B1, B2 etc. The other option is simple linear increments. If the first clone name is "lane1", the others will be initialized with lane2, lane3, lane4 etc..
Value range:
numeric 1..99
"numeric"
TRAY A1..H12
"tray"
lock direction
"lockdirection"
Parameter for the markerlock editor in Step 4. Depends on the origin of the logical well. The standard locking usually uses the loading well to lock upon (from left to right), but on an ABI gels it might be desirable to lock from the right, using the rightmost band as a starting point.
Value range:
from left
"fromleft"
from right
"fromright"
normalisation method
"normmethod"
Parameter for the marker locking. The default is linear. Non-linear normalisation would be used to map band positions from an ABI gel back to where they would have been on an autoradiogram.
Value range:
linear
"linear"
non linear
"nonlinear"
band height model
"bandheightmodel"
Parameter for the bandcalling. If you have steadily decaying band heights, (e.g agarose gel, no glycerol), then set band height to decaying. If bands heights are random, then use random.
Value range:
decaying
"decaying"
random
"random"
max. contiguous bands.
"maxcontig"
Parameter for the bandcalling. Controls the number of bands that can be assigned to an undistinguished blob. Set this to 1 if you are worried about over-calling. Higher values like 3 will permit the calling of bands on shoulders of peaks.
Value range: Integer number between 1 and 4
pixel ratio
"pixratio"
Describes the pixel shape in the raw image. Scanning equipment is likely to gather better pixel resolution along the lanes than along the well axis. This number shows how much more. For Amersham scanned autoradiographs use 4.0, for FluorImager gels use 0.5 to 1.0 and for ABI gels we found 15 to 18 to work well.
Value range: Floating point number greater than 0.
image rotation
"rotation"
Parameter for the image conversion. Specifies an angle in 90 degree steps by which to rotate the image when converting it from the raw image to the image observed on the screen. Basically you have to end up with an image where the lanes run horizontally. The Amersham scanned autoradiographs (.dat files) do not need a rotation angle, whereas FluorImager gels (.tif files) usually need to be rotated by 90 degrees.
Value range: Integer number 0, 90, 180 or 270
greyscale
"greymin"
"greymax"
Configures the contrast mapping. Only configurable by numbers in the project defaults dialog, but changeable using the greyramp tool for an individual gel.
These two values (left and right in the default dialog) correspond to the bottom and top value in the greyramp tool. Enter the values that make the gel look best in Step 1 and 2. Don not copy down the value shown in Step 3 or 4, as the greyramp mapping is shifted for to display the traces (which are background-subtracted).
Value range for both values: Integer number between 0 and 255.

Last modified : November 1999 Image 3.10

* quick link - http://q.sanger.ac.uk/7s1wo9mr