ChangeLog for TMAJ

Version 3.7.1 (released 2013-03-03)

  • add patientid to arraybuilder full details export
  • display OutsideSurgPathNumber in ArrayBuilder full details
  • add better lasso mask error message
  • add validatedBy field to blockusages
  • add numberOfSlidesSectioned field to ArrayBlocks
  • update notes on how to make a dev database; do deploys
  • Remove references about tmaj4

Version 3.4.3 (released 2011-03-23)

  • Particles debug in Filter mask weren't calibrated (bug fix)
  • Particles can be dumped for an entire session instead of image-by-image.

Version 3.4.2 (released 2011-03-17)

  • Drop-down boxes can now be entered as integers to speed up data entry.
  • Organs were listed twice in BlockUsages drop-down box (bug fix)

Version 3.4.0 (released 2011-02-16)

  • Internal software improvements. Upgraded from Tomcat 6 to Tomcat 7. Upgraded JDBC driver for MySQL. Made TMAJ compatible with MySQL 5.5. Updated documentation.

Version 3.3.2 (released 2011-02-08)

  • ImageManager App: Calibration of image analysis results is now possible. Before, results were based on a scale of 0 to 255, but now they can be adjusted to say a polynomial curve.
  • ArrayBuilder App: Export of multiple arrayBlocks at once is now possible.

Version 3.2.29 (released 2010-11-11)

  • ImageManager App: On debug for Particle Mask, the original image is consulted instead of the binary image.

Version 3.2.26 (released 2010-09-09)

  • ImageManager App: A "Index 'Masks UNIQUE (MaskName,IASessionID)' for table 'Masks' would not be unique" was reported when a filter mask was saved that did not have an input mask specified. Before saving, we ask the client to specify an input mask.

Version 3.2.13 (released 2009-06-15)

  • Specimens App: The export button merges fields with the same name.  This is useful for dynamic fields that both might be named something like "Primary Histologic Type".  Before, they were their own columns.

Version 3.2.11 (released 2009-06-04)

  • General: Fixed a MySQL bug in the data-panel.  Added notes for an Ubuntu installation (or general Linux).

Version 3.2.9 (released 2009-05-20)

  • Images App: Fixed recent bug: edu.jhu.tmaj.servlet.request.impl.ScoredImageDetailsRequest failed: java.lang.RuntimeException: No such dynamic enumeration: 0 (bgurel)

Version 3.2.7 (released 2009-05-13)

  • ArrayBuilder: Export got a NullPointerException if there was a blank spot and there the user had not yet clicked a blank spot.

Version 3.2.6 (released 2009-05-08)

  • General Bug fix: edu.jhu.tmaj.servlet.request.impl.UpdateRequest failed: com.sybase.jdbc2.jdbc.SybSQLException: ASA Error -194: No primary key value for foreign key 'ScoredImageEnums' in table 'ScoredImageData'.  This bug was caused when a scoring strategy with drop-down boxes was used.  To fix this bug, several changes in the how dynamic fields are saved were changed.  The use of "-1" in static enumerations was removed to prevent confusion. 

Version 3.2.5 (released 2009-05-06)

  • General Bug fix: In Oracle, there is a maximum of 1000 in a SQL statement IN clause: java.sql.SQLException: ORA-01795: maximum number of expressions in a list is 1000.  This was addressed in an externalFiles SQL statement and fixed.

Version 3.2.4 (released 2009-04-13)

  • Image Analysis: 6 new filter types added: Dilate, Erode, Open, Close, Skeletonize, and Outline
  • Improved Filter GUI

Version 3.2.3 (released 2009-04-09)

  • Image Analysis: 2 new filters added: Watershed and Fill-Hole

Version 3.2.2 (released 2009-04-03)

  • Image Analysis: Particle Counting Filter added

Version 3.2.0 (released 2009-03-27)

  • Image Analysis: Particle Counting Feature added.  (beta)
  • Support for CLOB datatype in Oracle
  • Several fields added to Specimens table
  • New version uploaded to sourceforge.

Version 3.0.22 (released 2009-01-28)

  • Images App: Thumbnails are now cached.  ArraySlides with thumbnails are now much faster.

Version 3.0.21 (released 2009-01-21)

  • Specimens App: Added "Processing" field to specimens table

Version 3.0.20 (released 2009-01-20)

  • Images App: Fixed Link button
  • Specimens App (Tables in general): Moving around columns made column selection appear wrong.

Version 3.0.19 (released 2009-01-08)

  • Specimens: Added several fields to specimen tables for tracking slides and blocks. (hfedor)

Version 3.0.18 (released 2009-01-02)

  • ArrayBuilder: Added new color-coding feature for cell lines.

Version 3.0.16 (released 2008-12-17)

  • Added a new core-view to ArrayBuilder in which one can see the details of a cell-line

Version 3.0.15 (released 2008-12-15)

  • Added feature to ArrayBuilder where one can select multiple cores and then click the details button to reveal them.  (Before one could only get details for one array-core.)
  • Added a forwarding button called "CellLines" that would automatically show one the tissuediagnoses in the cell-lines frame.

Version 3.0.9 (released 2008-09-04)

  • Fixed problems in import app for Ariol Machine

Version 3.0.0 (released 2008-07-24)

Major Changes:

  • Addition of Image Analysis Capabilities to TMAJ (integrated the Frida Software program with TMAJ)
    • The Frida image analysis program has been integrated into TMAJ.
    • Frida can be accessed by going into the Images application and creating a new Frida Session
    • The results of the image analysis can be immediately viewed in TMAJ; this data can be viewed side-by-side with the user-assigned scoring data in TMAJ.  Thus we have automated image analysis combined with scores assigned directly by pathologists.
    • The Data Table in the Images application has an improved GUI for viewing data from multiple areas: specimens, blocks, tissue-diagnosis, array-cores, array-images, scored-images, machine scored data, and image analysis data.
  • Importing Images is significantly easier. 
    • There is no longer any need to compress images with ThumbsPlus.  This is done automatically with TMAJ.
    • All Images are automatically uploaded to the proper place on the server without having to manually place them there.
    • There is no longer any need to manually name directories to a proper array-block/ array-slide/ scan
    • Images are kept track of in the database to prevent accidental deletions or modifications
    • Images are automatically downloaded to the client for improved speed.  Before this had to be manually done.

Version 2.32.0 (released 2007-06-29)

  • Importing data from Frida (an Image Analysis Program) is much faster.

Version 2.30.0 (released 2007-04-13)

  • Added support for group admins.  Group Admins is a level of security between regular users and administrators.  They have control over a subset of specimens, arrayblocks, and projects.  They may grant access to other users.  Group admins are assigned a subset of users; they can then assign permissions to these users.
  • Added an AccessPatientData permission for all Users.  To be able to see patient information, the Display_Patients_Tab in the file must also be set to true.

Version 2.29.0 (released 2007-04-03)

Images App

  • Support for Image Analysis.  Integration with separate image analysis program (Frida) completed.
  • Merged Machine Scores and Regular Data Table

Version 2.27.0 (released 2007-03-12)

General / Database

  • Color-Scheme in ArrayBuilder is no longer hard-coded.  It may be set by modifying a row in the KeyValues table called ARRAY_COLORS
  • No enumerations are hard-coded anymore.   All simple enumerations (like block-status and block-fixation) now are retrieved from the Enumerations table in the database.  Previously some of these had their own table (like SpecimenFixation.)  Others were hard-coded in the source-code.  Now they can all be changed by simply modifying the Enumerations table in the database.

Version 2.26.0 (released 2006-11-01)

Specimens App

  • Added support for cell lines and xenografts
    To access Cell Lines:
    1. Log onto TMAJ as a user permission to access the specimens application
    2. Click the Specimens App button to launch the specimens application
    3. Go to the Specimens Tab
    4. Click the Extras... Button
    5. Click the Cell Lines button

      You will now be able to enter information about cell lines, cell line experiments and xenograft experiments.  You will also be able to assign a TissueDiagnosis to a cell line experiment. 

Version 2.25.0 (released 2006-09-13)


  • Added support for Microsoft SQL Server database

Version 2.20.0 (released 2006-07-26)


  • Added support for MySQL database

Version 2.13.14 (released 2005-10-24)


  • Added feature to limit user access to gross description in the Specimens App [H Fedor]

Version 2.13.4 (released 2005-08-11)

Specimens Manager

  • Added ability to check the Arrays to which a TissueDiagnosis belonged.  [H Fedor]
    1. Go to the Specimens Manager application
    2. Go to the Tissue Diagnosis Tab
    3. Search for a tissue diagnosis, and then highlight it.
    4. Click the ArrayCores>> button

Array Manager

  • Added BarCode field to the Scans table.  This allows a person to determine the details of an ArraySlide just by knowing the BarCode. [Kristen]

Version 2.13.3 (released 2005-08-01)


  • Added a feature where a triple click on a table splits the tab into several frames
  • Added TMAJ logo to main application window and about dialog.

Version 2.13.1 (released 2005-07-14)

ArrayManager Application

  • Created this application by moving the ArrayBlock, ArraySlide, and Scan tab from the administrator application.

Version 2.13.0 (released 2005-07-13)


  • added Hopkins icons to login screen

Specimens Application

  • Added support for Slides table

Version 2.12.0 (released 2005-07-01)


  • merged applications into one
  • created config files to allow for TMAJ executable-form distribution

Images Application

  • Fixed "polygon error" in drawing application so that polygons with more points could be drawn

Version 2.11.2 (released 2005-06-10)

Images Application

  • Color coded the Data Table Window, both in the table and in the hide-columns popup

Version 2.11.0 (released 2005-05-31)

Admin Application

  • Added MetaData application to Admin app. MetaData is currently read-only.

Version 2.10.5 (released 2005-05-17)

Specimens Application

  • Add-Row Feature added: If you press the shift key and click the "add row" button, the row that is currently highlighted will be copied to the newly added row
  • Cut/Paste feature added.  Click on the primary key of a row, (e.g. the SpecimenID), and click CTRL-C.  Next highlight the row you wish to paste to and click CTRL-V.
  • Surg Path Number Generator feature added.  The feature was added solely for the purpose of the Animals application.  It can be used to generate Surg Path Numbers. 

Version 2.10.2 (released 2005-04-28)

Specimens Application

  • enumerated Hospitals field for increased data intregrity
  • made PatientID field mandatory


  • Added CachedDynamicMetaData class

Version 2.10.0 (released 2005-04-25)

Animals Application

  • Created this application.

Version 2.9.0 (released 2005-04-12)

Samples Application

  • Created this application

Version 2.8.5 (released 2005-03-03)


  • Extended Javadoc Documentation
  • Reorganized the database and command packages
  • Renamed some classes that had a confusing name.

Images Application

  • Added a "Show only Filtered Rows" for the Machine Scores Table.  [Faith]
    This means that a user can filter rows out in the DotDataTable, then go the Machine Scores table, hit the "Show only filtered Rows" button,
    and only see the rows that were filtered out.
  • Enabled deletion of sessions that have data in them.  [De Marzo]
    Note: Only administrators can use this feature. Regular users will only be able to delete empty sessions.
    A warning in a red font is shown to warn administators before deleting a session.

Version 2.8.2 (released 2005-02-25)

Import Application

  • Support for multiple thresholds on MachineScoredData added
  • To import new Machine Scores:
    1. Make sure the file is named properly, according to the directions in the Import documentation webpage.  For example:
    Note: The 10th position should give a description about the MachineScoringSession. In this case it is threshold52.
    2. Open the excel file in Excel, then choose "Save As"
    3. Remove the quotes that appear at the beginning and end of the fileName.
    4. Refresh the "Save As Type". First choose any other type like "XML Data",then choose "Text Tab Delimited".  The filename in the "Save As"
    dialog should have a.txt extention.  Click the save button to save a new .txt file.
    5. The file is now ready to be imported.  Open the import application and go to the "Machine Scores" Tab.
    6. Choose as many files as you like to be imported and then the click Start button.  Make sure you are choosing the .txt files you created in the above step and not the original .xls files. No dialogs are used, and thus all messages to the user appear in the message box at the bottom.  This allows many files to be quickly imported without the user having to click "okay" for an confirmation message.

Version 2.8.1 (released 2005-02-20)

Import Application

  • Machine-Scoring Sessions can be deleted. [Faith]
  • Machine-Scores Import made into its own Tab. 

Images Application

  • Machine Scores for ALL sessions may be viewed. [Faith]
    1. Log on to the images application
    2. Locate the Menu of the Project Frame and go to Tools -> Download Data
    3. Highlight the sessions whose Machine Scores you wish to View
    4. Click the 'Download Machine Scores' Session. 
    This can be linked with normal session data by linking the ArrayImageID field.

Version 2.8.0 beta (released 2005-02-18)


  • Infostructure for multiple thresholds on Machine-Scored Data added.  [De Marzo]
    Note: Until the next version, the database will still enforce the one Machine-Scored Session per Scan. 

Import Application

  • TextArea used instead of dialogs to make Machine-Scored Data imports quicker.

Images Application

  • Machine-Scored Data Table GUI added,..  [De Marzo]
  • Lineup feature added  [Faith]
    Images in a session can be lined-up by going to the Dot-Table-Frame, sorting the rows, and then clicking the Lineup Button.
    Note: The lineup feature will not work for all scans, as most have not had Mid-Size images created for them yet.
  • Fast Invalidation of Machine Scores.  [Faith]
    1. Open the Images application
    2. Open a session whose scan has Machine-Scored Data
    3. Download the MidSize images to your local hardrive.
        Menu of ArraySlide Frame -> Tools -> Download -> MidSize Images
    4. Open the Machine Scores Table
        Menu of ArraySlide Frame -> View-> Show Machine Scores Table
    5. Click the Lineup Button.
    6. Click on an images you want to make invalid.
        The images you select will be highlighted in green.

    7. When finished, click the "Filter For Selected Images" button. 
         The Machine Scores Table will now only show the images you selected.
    8.  Select all the rows in the table by clicking CTRL-A.
    9.  Click the "Set Valid Status" button, then click Invalidate.

Version 2.7.16 (released 2005-02-14)


  • Old JHU logo removed from documentation [Brumbaugh]
  • Primary_Histologic_Type changed to HistologicType (Input & Images Application.)

Import Application

  • Wipe Gross Description feature completed.  [Fedor]

Input Application

  • Bug Fixed: Dynamic enumerated fields could not be set to NULL after having been given a value.

Images Application

  • Users are now warned before they change a session's scoring strategy. [De Marzo]
  • Changing the Notes field results in a "O" for the coordinate (as opposed to an X or / or nothing) [De Marzo]
  • ArraySlide Frame X's made larger [De Marzo]
  • AutoScoredData changed to MachineScores [De Marzo]
  • Bug Fixed: Navigator failed if coordinate (1,1) was marked as Bad [De Marzo]

Version  2.7.14 (released 2005-02-07)


  • New code added in build.xml and Constants package that allows easy switches between the different versions of TMAJ.

Images Application

  • New text-legend on ArraySlide Panel.  Before, an "X" simply meant the image had been scored in one way or another.  Now there is:
    /  -- a type has been entered
    X -- a type and diagnosis have been entered
    O -- other information besides a type and diagnosis have been entered

Version 2.7.5 (released 2005-01-31)

Images Application

  • Fixed Published Sessions Error: Database was not updated when user tried to publish a session.

Version 2.7.4 (released 2005-01-28)


  • Logging feature added.  Log of records can be viewed by clicking History Button.

Input Application

  • Updated Sort Filter Frame to allow for more advanced searches.

Images Application

  • Invalidation of AutoScoredData feature added.
  • All-Sesssions Data Panel: SharedTo Field allows user to view which sessions have been shared out.

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