Information Flow Summary
- A new user is added.
The user is assigned a password, and given permissions to access
specified regions of the TMAJ program.
- Specimens are put in the
database. This can happen in two ways.
A) Specimens can be entered by going into the
input application and manually
entering a Specimen. This is done
by opening the Specimens Application, going to the Specimens tab, and
clicking the Add button. The patients table is ignored, and the
foreign key PatientID in the Specimens table is given a default
value. This is the most common way data input starts off in
Steps: The user must be given permission to access the Specimens
Application before this can happen.
B) Alternatively, the user can import a tab-delimited file in the Import
Application. If the user were at hopkins, the tab-delimited
file would probably come from PDS
(Pathology Data Systems), a
centralized Johns Hopkins data system for storing specimens that come
Surgical Pathology. However, the Import application can be
configured for different types of sources. In a tab-delimted PDS
file, each row represents a case. A case is a combination of a patient
and a patient's specimen. In the specimen-import, both the
and Specimens table are populated. This is the only way the
patients table is modified in TMAJ. Also, a
user can import a tab-delimited file of specimens. This
tab-delimited file is obtained from PDS, a centralized Hopkins data
system for storing specimen information. Note: This is a weaker
area of TMAJ, and we intend to upgrade to a more robust system using
XML to do imports.
- Blocks and Tissue Diagnosis's
(Sub-Blocks) are put in the database. Blocks and
TissueDiagnosis's must be manually entered through the Specimens application.
- A new ArrayBlock is entered.
This is done in the ArrayBlock
Tab of the ArrayManager application.
- The ArrayBlock is Designed.
The arrayblock is designed in the ArrayBuilder
the user chooses an ArrayBlock. Next, for each coordinate in the
arrayBlock, the user assigns a tissueDiagnosis.
Note: Steps 1-3 are often combined into one with the "Express Entry"
feature. Basically the user just selects a coordinate, enters
minimum information about the specimen, block, and TissueDiagnosis, and
all 3 are created on the fly, with the generated TissueDiagnosisID
being assigned to the coordinate.
Steps: The user must be given permission to the ArrayBlock. Open
the Admin application, and then click on the UsersArrayBlocks tab.
- An ArraySlide from the
ArrayBlock is cut and scanned. This step is physical in
nature, and is performed by
the tma technicians. An ArraySlide is cut along the
z-axis on an ArrayBlock. The ArraySlide
is scanned using a
scanning machine and the images are dumped into a directory on the
machine. A scan of an ArraySlide will output 1 directory, with
about 400 jpegs inside it (the arrays are often 20 by 20).
Each JPEG file represents a coordinate on the ArraySlide, and you will
see an X and Y position number in each of the image filenames.
- The jpeg images in the directory
just created are imported into TMAJ. Go to the
"ArrayImages" tab on the Import
application. Choose the directory
that contains the ArraySlide's scanned images, as mentioned in the
previous step. Make sure that:
* The directory is in the appropriate place (in the [[main images
* The directory is named using the scan
This program populates the ArrayImages table.
Optional Step: Sometimes you will be asked to import machine-scored
Data. Machine-Scored Data
are scores that are automatically assigned to images by the scanning
machines themselves. For example, this data might be how
much "blue" or "brown" there is in an image. To do this, click on
the "MachineScoredData" button in the import application, and choose
file that contains the tab-delimited machne-scored data. Make
the filename is in scan standard format.
Machine-Scored data will
show up in the DataPanel and InfoPanel in the Images application.
- The ArraySlide is assigned to a
Project. If necessary, a new Project is created. Note: You
may skip this step if you added the ArraySlide to a project while doing
A project is a collection of
ArraySlides. In addition, there is a UsersProjects table that
links Users to Projects. Thus, Users are linked to Projects, and
Projects are linked to ArraySlides--in effect, an administrator can
control what Users can see what ArraySlides. A new project
can be created in the Projects
tab of the Admin application.
Users are assigned to that project in the UsersProjects tab.
ArraySlides are assigned to that project is the Projects-ArraySlides
tab. The step is always performed by a TMAJ administrator.
- Create a Session. A
user logs on to the image manager
application. If the end-user hasn't done
so already, they must first create a new session. A session is a combination of a Scan
and a User, and represents a user's scoring of an scanned
ArraySlide. Thus, a scan can be scored multiple times, by
different users, at different times. A user can even decide
rescore an scanned ArraySlide with a different session, thus keeping
for both sessions.
Admin Steps: You must have created the user and given permission to
access the Images application.
- End-Users assign their own
scores to the images. A user then
double-clicks on the appropriate
session to open the ArraySlide
and the current ArrayImage, on position x=1, y=1. The user presses
the next button until all the images are scored.
- Session is published.
After a user has finished scoring a session, the session may be
published so that the data can no longer be changed, and that all users
may see. Alternatively, a user may finalize the data, which
ensures that the data will not be modified.
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