Import Application

Importing ArrayImages

Please click the link above for more information on importing array-images.

MachineScores Tab

Machine Scored Data refers to scores that a machine automatically assigns to an ArrayImage.  (This is in contrast to scores that users assign to images.) Machine Scored Data used to be called Auto Scored Data.   For example, the Chromavision machine might assign the following scores to one ArrrayImage:
BrownArea: 105
BlueArea: 1304
BrownIntensity: 75

Importing MachineScores into the database is optional.  They simply give the user more information about the ArrayImage.  The MachineScores for an ArrayImage can be viewed by clicking the "Info button" on the ArrayImage Panel, or by clicking the "Show Machine Scores Table" on the ArraySlide panel.  Both of the panels are viewed in the Images application after one opens a session.

The machine scored data for an ArraySlide is put into a tab-delimited text file by the Scanning Machine.  Before the file can be imported, it must be renamed properly.  The naming format used is the same as the naming format used for directories of ArrayImages (ArraySlides).  An example machine-scores file may look something like:
The only difference is the 'extra information' section gives a description of the MachineScores, in this case 'Threshold5'.

More details on MachineScores: MachineSessions

A MachineSession represents one Machine-Scoring of an ArraySlide scan.  The entire .txt file represents a MachineSession. It should be noted that it is possible for an ArraySlide Scan to have multiple MachineSessions.  So for example, ArrayImage#123 would end up having several values for BrownArea.
BrownArea: 105  [MachineSessionID#5]
BrownArea: 271 [MachineSessionID#6]

The 'short description' section in the filename should give adequate detail in describing each MachineSession if there is more than one MachineSession per scan.
For the case of MachineSessions, the short description will differentiate among the machine sessions for the scans.
For example:
In the above example, the short description shows that each machine session uses a different threshold.

Specimens Tab

Specimens can be imported into the database by importing a tab-delimited file.  Each row in the file represents one specimens.  Currently this feature is only supporting at JHH.  This tab-delimited file is obtained from PDS (Pathology Data Systems).  This file can be imported as-is in the import application:
1. Launch the import application
2. Choose the Specimens tab.
3. Select the Hospital where the specimens are located.
4. Choose the PDS tab-delimited file. 
5. Click the start button.

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