Specimens Manager Application

The specimens manager application enables the entry of patient, specimen, donor-block, and tissue diagnosis information. Optionally information about slides and blockUsages may be entered as well. The Slides and BlockUsages tables are extraneous tables, meaning it is possible to run TMAJ without putting data in either one of them.

Background

TableEntry Explains how to use the TMAJ table entry
Tissue MicroArray Basics -- Defines the words specimen, block, and tissue diagnosis
Database Tables

Patients Tab

A patients tab where patient information may be entered is optional. This can be enabled in the config file. By default it is turned off.

Specimens Tab

The specimens table is one of 3 dynamic tables in TMAJ. A dynamic table means that it can have organ-specific fields. Specimens can also be put into TMAJ in the [[import application]].

To add a new specimen:

Click the Add button
You will be prompted with a list of specimen types. Depending on which type you choose, fields specific for that organ will come up. In this example we will choose specimen type "Radical Prostatetomy".
Fill in all the required fields. (Required fields appear in bold.) Notice that organ-specific fields will appear in italics.
Click the Save button.

A list of specimen-types from which to choose. The choice will determine which organ-specific fields are displayed. (Step 2)

Specimens Entry. The fields in italics are specific to the specimen type "Radical Prostatetomy". They include GleasonSum, HasSeminalVesicle, HasProstateFluid, and PreOpPSA. For another specimen type, such as kidney, these fields would be irrelevant. TMAJ is structured so that only the proper dynamic fields come up for the proper type.

To enter blocks for this specimen, highlight the row and then click the "Blocks >>>" forwarding button.

Blocks Tab

Adding a block. By switching to the Blocks tab, blocks can be entered and modified. Blocks is not a dynamic table, unlike Specimens and Tissue Diagnosis. The same fields will appear every time.

To enter TissueDiagnosis's for this block, highlight the row and then click the "TissueDiagnosis >>>" forwarding button.

Tissue Diagnosis Tab

Adding a Tissue Diagnosis. When the user clicks the add button, the user is prompted for the "Type". In this case, we choose "Prostate -- Carcinoma". Certain extra fields appear for this type. The dynamic fields are shown in italics. They include, p27Score, Prostate_Zone, and HistologicType. These fields are specific to the TissueTypeID "Prostate -- Carninoma".

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