Configuring Stainfinder 1.1 to work with Multiple Datasets
In Version 1.1 of Stainfinder, you may notice that the code referring to server path names have changed. This is to accommodate Stainfinder's ability
to access multiple datasets that are each stored in their own directory. For example, if your image database was located
in your server under the path /share/tissue/archive/scans/, and is accessible online via http://www.myserver.edu/scans/,
you would have configured Stainfinder 1.0 as follows:
my $rootDir = '/share/tissue/archive/';
my $webDir = '/scans/';
my $mainDir = '/share/tissue/archive/scans/';
So a user accessing a server running Stainfinder 1.0 would probably click on a case descripter in TreeView or on the "SF" button in CaseExplorer, a
new browser window is opened with a URL that may look like this:
http://www.myserver.edu/cgi-bin/Stainfinder.pl?uniqid=
4_35_4_5_35_1128_436.jpg*4_35_5_5_35_1128_437.jpg!1326!apod!CD34
(the URL is actually one single line; it's wrapped around to two lines here for ease of display)
In Stainfinder 1.1, however, you will notice that $rootDir has gone away, and that
there is now a new variable $dirname.
my $mainDir = '/share/tissue/archive/scans/'.$dirname.'/';
my $webDir = '/scans/'.$dirname.'/';
This variable gets passed in from the URL as the first
item in the URL. In such a situation, a user accessing the "myTMAdataset" TMA dataset on a server running Stainfinder 1.1 would in the process open a
new browser window with a URL that may look like this:
http://www.myserver.edu/cgi-bin/Stainfinder.pl?uniqid=
myTMAdataset!4_35_4_5_35_1128_436.jpg*4_35_5_5_35_1128_437.jpg!1326!apod!CD34
(the URL is actually one single line; it's wrapped around to two lines here for ease of display; the change is
highlighted in red bold text for clarity)
What happens is that "myTMAdataset" is passed into the Stainfinder program and stored into the variable $dirname.
Stainfinder will now look for images related to "myTMAdataset" in the following places:
my $mainDir = '/share/tissue/archive/scans/myTMAdataset/'
my $webdir = '/scans/myTMAdataset/'
The best place to configure your TMA Dataset to work with this feature of Stainfinder 1.1 is to append the dataset name to each value in the UID
column such that it begins with the name of the dataset, followed by an exclamation point. For example, if a given cell in the UID
column looked like this:
4_35_4_5_35_1128_436.jpg*4_35_5_5_35_1128_437.jpg!1326!apod!CD34
then you will want to change it to this:
myTMAdataset!4_35_4_5_35_1128_436.jpg*4_35_5_5_35_1128_437.jpg!1326!apod!CD34
This can be accomplished very simply by using an Excel formula like the following: "="myTMAdataset!"&A4"
(where A4 or its equivalent is the address that should point to the first cell in the UID column containing the dataset's unique identifiers).
In the combined PCL text file, copy and paste the formula for the entire dataset, and paste special as values back into the UID column.
Don't forget that the name of the dataset has to match
the name of the directory in which the images are stored. Also don't forget that if your server is running UNIX/Linux, names are
case sensitive.
Configuring Stainfinder 1.1 to display replicate cores
Configuring your image database to allow Stainfinder 1.1 to display replicate cores is actually quite simple. You will notice
that the example URL as shown above contains some extra information compared to an uncombined dataset, which in this case is an additional
JPG filename. Each of the JPG filenames refer to the individual core replicate images. These don't have to be stored within the same
subdirectories, but they do have to be present somewhere within the directory tree that contains all the images for the TMA dataset.
No additional action is required - as long as your directory and JPG filenames conform to the Bliss image system
nomenclature, Stainfinder 1.1 should be able to find and retrieve those images.
back to top
Back to the Stainfinder Update Section
Return to the walkthrough
overview page.
|
