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
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:
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)
- 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
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 client.properties file must also be set
Version 2.29.0 (released 2007-04-03)
- 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)
- Added support for cell lines and xenografts
To access Cell Lines:
- Log onto TMAJ as a user permission to access the specimens
- Click the Specimens App
button to launch the specimens application
- Go to the Specimens Tab
- Click the Extras... Button
- 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
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)
- Added ability to check the Arrays to which a TissueDiagnosis
belonged. [H Fedor]
- Go to the Specimens Manager application
- Go to the Tissue Diagnosis Tab
- Search for a tissue diagnosis, and then highlight it.
- Click the ArrayCores>> button
- Added BarCode field to the Scans table. This allows a
person to determine the details of an ArraySlide just by knowing the
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)
- 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
- 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
- Fixed "polygon error" in drawing application so that polygons
with more points could be drawn
Version 2.11.2 (released 2005-06-10)
- Color coded the Data Table Window, both in the table and in the
Version 2.11.0 (released 2005-05-31)
- Added MetaData application to Admin app. MetaData is currently
Version 2.10.5 (released 2005-05-17)
- 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)
- enumerated Hospitals field for increased data intregrity
- made PatientID field mandatory
- Added CachedDynamicMetaData class
Version 2.10.0 (released 2005-04-25)
- Created this application.
Version 2.9.0 (released 2005-04-12)
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.
- Added a "Show only Filtered Rows" for the Machine Scores
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
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
Version 2.8.2 (released 2005-02-25)
- Support for multiple thresholds on MachineScoredData added
- To import new
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
4. Refresh the "Save As Type". First choose any other type like
"XML Data",then choose "Text Tab Delimited". The filename in the
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
Version 2.8.1 (released 2005-02-20)
- Machine-Scoring Sessions can be deleted. [Faith]
- Machine-Scores Import made into its own Tab.
- Machine Scores for ALL sessions may be viewed. [Faith]
This can be linked with normal session data by linking the ArrayImageID
- Log on to the images application
- Locate the Menu of the Project Frame and go to Tools ->
- Highlight the sessions whose Machine Scores you wish to View
- Click the 'Download Machine Scores' Session.
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.
- TextArea used instead of dialogs to make Machine-Scored Data
- Machine-Scored Data Table GUI added,.. [De Marzo]
- Lineup feature added
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 &
- Wipe Gross Description feature completed. [Fedor]
- Bug Fixed: Dynamic enumerated fields could not be set to NULL
after having been given a value.
- 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
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.
- New text-legend on ArraySlide Panel. Before, an "X" simply
meant the image had been scored in one way or another. Now there
/ -- 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)
- 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.
- Updated Sort Filter Frame to allow for more advanced searches.
- Invalidation of AutoScoredData feature added.
- All-Sesssions Data Panel: SharedTo Field allows user to view
which sessions have been shared out.
© Copyright 2010 |
All Rights Reserved | The Johns Hopkins University