- Back to Most Recent SpotReader History
- Version 1.2.2.2 (January 27, 2005):
- New Features:
- Selecting features in a block by dragging a rectangle no longer selects the neighboring block boundary when that neighboring block boundary is touched. A block boundary is selected only if you select features in that block.
- Pressing > and < now takes you to the next or previous block even if you de-select the current block. Previously, if nothing was selected, > and < would take you to the first block. This could cause you to lose your place when inspecting the grid.
- Made it easier to move small features with the mouse. Previously, if you tried to move a small feature, you'd often end up sizing it instead.
- Database window now shows the name of the database file it is using.
- Block finding now finds blocks correctly when blocks are grouped. Previously SpotReader would only work with two groups. It now works with any number of groups as long as the groups have the same size. Grouped blocks look like this:
X X X X
X X X X
X X X X
X X X X
X X X X
X X X X
- In Pin Mode, placing two pins side by side is a special case to allow cutting a block into two pieces and moving the lower half independently of the top half. Previously this didn't work with the first two or last two features of a row. It now does.
- In addition to correcting translational misalignments, SpotReader can now correct for rotational misalignments between various colored images in one array. See Misc tab in Preferences to turn this option on.
- Bugs Fixed:
- The Manual grid dialog now defaults to 100 microns for feature spacings.
- The Manual grid dialog now defaults to rectangular grid layout.
- Feature viewer now shows a 3-digit block number correctly. The field was too narrow to show block numbers > 99. (Yes, there are arrays with more than 100 blocks.)
- Holding down the Alt key while clicking on features removes those features from the current selection. The image now correctly updates to reflect this.
- In Pin mode, the feature viewer now correctly shows the currently-selected feature as selected.
- Version 1.2.1.4 (December 24, 2004):
- New Features:
- Relaxed a condition that unnecessarily made the search for block boundaries fail in a certain rare cases.
- Changed the logic for how "Empty" flags were assigned. Previously if the gene name in the gene list was blank or "Empty" the empty flag was set. Now the flag is set if either the gene name or the gene ID is "Empty", or if both are blank. The new logic is more correct.
- Changed the way the Document Name is loaded from a TIFF file. The Document Name is used for the Comment header item in the results file. The document name sometimes had new-line characters in it, causing problems with the results file.
- Changed the User-Agent field in the HTTP request when getting a key over the internet. This may fix a problem one user had getting a key through a proxy server.
- Version 1.2.1.3 (December 13, 2004):
- New Features:
- Finding Block Boundaries: Improved code to handle certain cases that caused the search for block boundaries to fail with Orange-packed arrays.
- Bugs Fixed:
- Bug in Pin Mode with Orange-Packed arrays: Fixed a bug that forced part of a block to return to rectangular packing when moving a pin.
- Fixed a bug that caused the remaking of a grid with repositioned blocks to mess up orange-packing.
- Version 1.2.1.2 (December 8, 2004):
- New Features:
- Saving JPEGs: Option to save a JPEG image at the same time it saves results. See Preferences... Output Files Tab.
- GenePix 3 format Results: Option to save results in GenePix 3 (.gpr) format as well as GenePix 5 (.gpr) and SpotReader Results (.srr). See Preferences... Output Files Tab.
- Don't use sparse images in block finding: Program now checks the various colored images for spot information and doesn't use an image for block finding if it has little or no such information. Useful, for example, on DeRisi's Viro Chips where the sample image has only a few genes lit up.
- Improved Aligning on Previously Not-Found Spots: Improved the feature aligning to try a new aligning method on features that weren't found in the original aligning method. The result is fewer features not found.
- Manual Flags Made Visible: Features that have been manually flagged, or have been manually cleared of their automatic flags are drawn with a heavier circle or ellipse. So now it is possible to distinguish between features that are flagged automatically, and features that are flagged manually.
- Bugs Fixed:
- Not Saving Gene Names: Saving results automatically after processing in the database didn't save gene names with the results file.
- Clear Flags Except Empty: Clear Flags Except Empty command didn't clear automatic flags. It only cleared manual flags.
- Column Names in .gpr File: Previous versions would name columns in a .gpr file using "Ch1"/"Ch2" or "Red"/"Green" rather than wavelengths. For example "FRed Median" instead of "F635 Median". The .gpr file should only have wavelengths in columns.
- Version 1.2.0.2 (November 10, 2004):
- Bugs Fixed:
- If the image was cropped too tightly on the left or top edge, grid could fall off the edge of the image and the program would eventually crash.
- Fixed a resource leak that would cause the program to slow down over time.
- Version 1.2.0.1 (November 9, 2004):
- Bugs Fixed:
- Opening a grid made with version 1.1 caused part of the program to think it was orange-packed.
- Version 1.2.0.0 (November 7, 2004):
- New Features:
- Now does orange packed arrays (four variations on indented rows or columns):
o o o o o
o o o o o
o o o o o
- Added batch save of results file (Database | Save Results File(s)).
- Some improvements in individual feature aligning:
- All not-found features are reset to un-aligned position.
- Resetting to un-aligned position now works when doing F5.
- Not-found flags are now set when doing F5.
- Added new preferences (in the Misc tab of Preferences dialog):
- Max and min feature size settings.
- Turn off collision resizing while aligning features.
- Scatter plot on feature viewer now reflects color pair chosen for composite feature viewer. Axes colored accordingly.
- If you change flagging parameters while in Pin mode, it reminds you once that flags don't display in Pin mode.
- New graphic in the About SpotReader dialog.
- Bugs Fixed:
- Crashed sometimes when adjusting flag parameters.
- Hung sometimes when editing the grid.
- Fixed two bugs with finding blocks that caused SpotReader to fail on some arrays.
- Eliminated a memory leak when writing results file.
- Color-pair menu on feature viewer didn't reflect active setting.
- Finish flagging dialog is now modal.
- Flagging Parameters dialog was enabled while grid was being made.
- After editing a File Association, and setting the parameters on all matching entries in the Database, it deleted the image names from the parameters Results Table tab.
- Check blocks report dialog no longer shows if no grid present.
- F5 aligning is now the same as aligning done with New Grid...
- Improved error reporting when opening a bad gene list.
- Version 1.1 History
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