Changes and updates in Spotfinder 3.1.0, all paltforms

September 2005

New Features and changes

1. Full support for 8 bit tiff images was added. Those images can now be loaded and analysed in the same way as standard 16 bit tiff images.
2. Undo and Redo functions for grids have been added to ALL GRIDS and GRID menu on Analysis Page.
   Currently 3 levels of undo/redo are implemented.
3. Flag "U" was introduced in Spotfinder reported flag set. It is a flag intended to distinct the spots excluded from analysis by user (U for user) from spots not detected by spotfinding procedure (Z flag).
4. Cell center coordinates X and Y have been added in Spotfinder Data Page and output MEV file.
5. The "Grid indices" indicator was added to the status bar at the bottom of the program window toinform user about the current grid under the mouse pointer on Analysis Page.
6. Arrows buttons have been added to the Analysis Page navigation bar to provide sequetial scroll accross grids in addition to the existing random grid selection using  a grid button array.
7. Grid construction dialog evaluation  was changed to allows entry values up to 500.
8. DBIDs now can be set to Data Page spreadsheet and MEV file independently from UIDs. DBID column follows P-values columns in MEV file generated by Spotfinder.
9. Large step for the manual grid alignment was introduced. Since now user may speed up grid movement, rotattion , expansion and cell size changing by pressing and holding CTRL key when operates with keyboard arrow keys. Step size is increased by factor of 10 compare to the arrow key operation without CTRL key.
10. Grid drawing was redesigned for MacOSX. Now the grid cells are displayed correctly independently of the cell size change or the grid stretching. The user excluded spots/cells are displayed on Mac with a diagonal crossed because the coloring of dynamic (movable) objects (grids) is not supported on Mac.	
11. Due to the TIGR experiments with four color arrays the special four channel setup functionality, introduced in version 3.0.0 (see doc and readme file in 3.0.0 release for details),  was replaced by default four channels operation.
 
Bugs fixed

1. P-values are calculated in more consistent way now.
2. Fixed a bug where the use of contrast/brightness controls after swapping images in channels A and B would cause images be displayed as before swapping.
3. Fixed incorrected labeling on RI plot in the PDF report. It was log2(B/A), the correct is log2(A/B).
4. Fixed a bug which caused the program crash when user tries to apply a grid adjust procedure to the grid located too close to the image edge. While the image as this is still undesirable for procedure performance itself the program survives the bad conditions run and remains stable now.
5. Fixed a bug which generated MEV file with misplaced columns for one color set-up.
6. Fixed GAL file annotation file loader. Now GAL file with appended DBID column can read correctly and DBID canbe inserted in output MEV file.
7. On Compose Grid dialog the limits for row/column number have been increaded up to 500 to allow subgrids up to 500x500. Be carefull however to use this grids since the GUI response is slow this this big object.   
8. Fixed bug and improved program stability when grid is moved away from image area at alignment and processing steps.