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Release Notes
The following list shows a history of the development and the major changes of previous versions of ROXAS
.
1 April 2016 - v3.0.0
- Added new parameters: Mork’s index (new in overall and summary), mean hydraulic diameter (new in individual output), radial and tangential cell lumen diameter (with respect to X/Y origin), bending resistance index (t/b)2, Angle of cells’ major axis compared to orientation towards X/Y origin
- Added a new functionality to measure the length, width and projected area of scanned (conifer) needles.
- Added AOE classification “poor sample quality”, “pith”, “crack”, “needle outgrowth”, "resin duct"), percentage of poor quality AOE in ring deciles
- Allow JPG2000 files (*.jp2)
- When re-opening analyzed image, load backup cell and ring files as a second priority if no other file found.
- Cell extraction: improved the color filter; now the user can also define the upper limit (used to be fixed at 255), and one can define a cell size range for which to perform color filtering
- Adjust Protrusion filter to work in images with many (<32,768) protrusions by using an AOI / sub-image approach
- Cell wall thickness: allow to select/deselect visualization with circles, make the number of visualized cells customizable (Advanced settings > Miscellaneous); will be saved to ROXAS output files, can also be saved to configuration files
- Cell wall thickness: implement separate threshold for radial and tangential walls
- Improved earlywood border cell cleaning algorithm
- Improved ring border cleaning for linear samples: scale angular filter levels to image limits
- Configuration & Manual editing: added additional colors to the different object outlines, allow to adjust colors of more objects
- Manual Editing: added new toolbox with cell filtering: cell lumen area, aspect filter (elongated objects oriented towards X/Y origin), small cell outliers, color intensity, protrusions into cell lumina
- Manual editing: allow to define several polygons in Delete (lasso) cell(s)
- Angi’s Button: add listbox to see and adjust the list of ROXAS output files for which to batch adjust some settings (for batch re-calculation)
- Summarize ROXAS Output: added listbox to see and adjust the list of files to be summarized. Includ-ed also buttons to arrange the files in the correct order
- Summarize ROXAS Output: added option to exclude the first (incomplete) year; most useful in linear samples
- Settings, Cell Extraction: added a button to show/hide junk objects to ease creating a new ROXAS configuration
- Settings, Cell Extraction: automatically update the values in the text boxes if adjusting the thresholds for Restricted Dilation and Segmentation during calibration.
- Outlier Search: added hotkey control to move from one cell to the next using ALT+X
- Outlier Search: added option for inverse sorting (looking for small outliers)
- Added horizontal scroll bar in batch processing listboxes if items are too long
- Streamlined
image handling to avoid memory problems when working with larger images; this increases stability
- Include the components MSCOMCTL.ocx in the distribution file, since it is not installed on all PC’s (not sure it is really needed after removing the standard progress bar…)
- Show progress bar for all time consuming steps, also image processing, cell extraction and sub-image editing
- Fixed limitation in naming of analysis folders: allow “JPG” and other extensions to be part of the folder structure without confusion ROXAS
- Fixed bug in spatial calibration: in regional settings with comma as decimal separator, a comma was written to *.cal in the pixel/micron line, which IPP interpreted wrongly; now, ROXAS forces to always write a dot (“.”) instead of a comma (“,”).
- Fixed bug in window handling: when closing a window, ROXAS now performs a sensible action instead of just hiding the window; for example, closing the ROXAS main window now properly quits the ROXAS application with no ROXAS.exe in the Windows Task Manager.
- Several smaller
improvements of user friendliness
- Bug fixes and general improvements of stability
30 October 2014 - v2.0.0
- Changed licensing: now only one full version for all users after registration
- Added cell wall
thickness measurements for conifer analysis (and fibers in angiosperms, in some
cases)
- Added Mork’s index (ratio of cell wall thickness to lumen diameter,
‘thickness:span’). See Denne, 1989, IAWA Bulletin 10:59-62, formula 1
- Implemented Area of Exclusion (AOE): The user may add one to several
polygons to define regions to be excluded from analysis, also when calculating
area-based statistics such as conduit density. The AOE(s) are allowed to
overlap with AOI(s).
- AOI: do not perform check for conduits outside
of AOI when loading a previously analyzed image. When adding an AOI posthum,
the extraction of the AOI-conduits is done when (re-) calculating the output.
-> speeds up loading large images
- Spatial Calibration: created a new spatial calibration window with only
the relevant information to failure-proof this step
- Correct wrong spatial calibrations in linear samples by
automatically adjusting the Origin while keeping existing ring borders at their location.
- Batch Spatial Calibration:
select a folder for which all images (incl. those in subfolders) without
spatial calibration file can be easily calibrated in sequence (values from
previous image are transferred to next as a suggestion). In cores, the user is
asked after the first image whether to apply the pixel/micron resolution to all
remaining images (usually the case) for fast spatial calibration.
- Batch Create Project
File(s): select a folder (incl. subfolders) in which a project file for batch
processing can be created for each image. Specific settings for analysis can be
automatically assigned for all images. If no AOI or AOE is required, creation
of project files is done without any further user interaction after the first
image.
- Batch Run Projects:
now the user can define the target folder (incl. subfolders) and ROXAS
automatically identifies the images with a project file.
- Angi’s Button (new):
Change one to several values in all Excel Output Files in specified folder
(incl. subfolders) for batch re-calculation. This may be useful if adjusting
some parameters such as changing from angiosperm to conifer analysis
(calculation of cell wall thickness!)
- Summarize ROXAS
Output: Subfolders of the selected folder are now included as well in
summarizing
- Summarize ROXAS Output: new columns for metadata such as ROXAS version,
user, spatial calibration settings etc.
- Summarize ROXAS Output: data from samples with overlapping rings can be merged using an averaging or a excluding option.
- Prevent merging of conduits when using the convex outline filter
- New filter for
conduit extraction: color intensity range in original color image can be
specified to exclude pseudo-conduits. This can be used, for example, to exclude
blue-stained ray cells when using a safranin – astra blue staining.
- New filter for
conduit extraction: remove protrusions into cell lumina (e.g. disrupted secondary
cell walls in conifer tracheids)
- Manual Editing:
Option to load ring borders from a text file. This option is useful if user
forgot to calculate the Excel output after manual editing. Before, the ring
traces could not be loaded anymore. Now, the user should skip automatic
analysis with all the other settings of the main window being correct. He
should then push Update outlines in the Manual editing window to load the ring
traces from any existing file (conduits have to be loaded first!).
- Manual Editing: Added tool for guided quality control of the largest
conduits (‘Outlier Search’). Accessible from Manual Editing Utilities &
Options. The conduits are internally sorted from largest to smallest and ROXAS
moves the window from one to the next upon pushing the forward button. The
conduits are highlighted with a target. The user can then edit the identified
conduits (e.g. to split erroneously merged conduits) using the normal manual
editing tools.
- Manual Editing, Sub-image analysis: added annual ring borders and sector
limits for sub-images
- Advanced
Settings > Miscellanous: new option to additionally save ROXAS Excel output (Overall summary,
Annual rings, Vessels) as text files
- New progress bar
that gives the user a feedback about progress of larger processes
- Several smaller
improvements of user friendliness
- Bug fixes and general improvements of stability
17 September 2013 - v1.6.0.0
- ROXAS main window, Batch
processing: new option to recalculate output of previously analyzed images.
This option is useful when parameter calculation was improved (see below) or
extended to quickly create updated Excel output files.
- ROXAS main
window, Summarize ROXAS Output:
new option to restrict overall summary to specific years (period).
- ROXAS main
window: periodical appearance
of a button to delete the “IpRef.cal” file that stores the used spatial
calibrations; when this file gets too large, loading and creating spatial calibrations - and therefore analysis in general - slow down.
- Spatial calibration in cross-sections: the default location of the cross-hair specifying the center of the
sample is now in the image center.
- Manual editing: moved
the ‘Change the checkpoint resolution of ring borders to ...’ option to the new ‘Editing Utilities &
Options’
- Manual editing: moved the
‘Show/hide Settings’ option to the ‘Editing Utilities & Options’
- Manual
Editing, Editing Utilities &
Options: new option to
split the image into overlapping sub-images; this speeds up conduit editing in
very large image files and avoids a bug of IPP that does not support the Magic Wand
tool for conduit drawing in very large images.
- Manual
Editing, Editing Utilities &
Options: new option to represent the outlines of conduit lumina as filled objects and to customize the
outline color
- Manual
Editing, Editing Utilities &
Options: new option to automatically show and hide
conduit outlines for a customizable number of repetitions and a customizable repetition
rate
- Improved algorithm for ring width
measurement in rings with oblique and non-parallel borders as often appears towards the
stem center. The obliqueness of both the inner and outer ring border is now independently considered. Before, only the obliqueness of the outer ring border was considered, assuming the inner border would
run more or less parallel.
- Improved algorithm for
assigning conduits to annual rings: now interpolating between checkpoints of ring borders. Before, conduits
were related to the closest checkpoint.
- Improved algorithm for
detection of touching neighboring vessels (vessel grouping): take angle of major
axis into account.
Before, vessels were always assumed to touch with their flat side (the major
axis).
- New output (in summary
file): mean hydraulic diameter
- New output (in summary
file): vessel group size frequency distribution (absolute and relative)
- New output (in summary
file): relative position of largest/smallest conduit and max3 within annual
ring
- Generally streamlined
automatic analysis to better handle very large images.
- Bug
fixes and general improvements of stability.
14 March 2013 - v1.5.0.0
- ROXAS main window: added
function to summarize all ROXAS output files of a folder and
together with additional statistics such as percentiles of conduit size,
conduit size
contributing xy% to theoretical conductivity, conduit size frequency
distribution and percentage of grouped conduits depending on conduit
size
classes
- Manual editing: enable to draw several missing rings in one go.
- Manual editing: speed up redrawing of conduit outlines that were added using the trace tool.
- Manual editing: replaced some of the old instruction windows (draw new ring, split conduits, draw conduits) by windows
that can be represented in minimal view and stay in place after moving from the
central startup position to a more peripheral position. This avoids obstructing
any image target regions when editing
- Advanced settings: omit conduit grouping
analysis if double cell wall thickness is set to 0 to speed up processing. This adjustment may be
particularly sensible in coniferous wood
- Enable writing output in Excel format 2007 and higher (*.xlsx) if present. In Excel
2007 and later, the maximum number of columns and rows is much higher (up to 16,384 columns and 1,048,576 rows), which allows to
write data from much larger samples. If you load a previously analyzed image and do some editing, there will be a
new *.xlsx output file besides the old *.xls file. The latter can be deleted.
- Make
ROXAS fully independent from MS Windows Regional Settings (allow any
regional settings for import/export/exchange of ROXAS settings files and
Excel
output files). In earlier versions, some Regional Settings (e.g., NL,
RU) using comma (",") instead of point (".") as a deliminator for
decimal numbers caused problems.
- Bug fixes and general improvements of stability.
8 November 2012 - v1.4.0.4
- Tree cores: implemented automatic origin selection during spatial
calibration.
- Tree cores: improved algorithm that adjusts ring width measurements to inclined (non-horizontal) ring borders; should give more accurate values than before
- Manual editing: added functionality to change checkpoint resolution of
ring borders
- ROXAS project files (*.rpf) still work even after moving to another
folder as long as the associated image and spatial calibration files (*.cal) are
moved as well. Before, the image path in the rpf-file had to be updated
- Bug fixes and general improvements of stability and user friendliness.
5 June 2012 - v1.4.0
- Decoupled all previously coded species specific settings to settings files (*.rsf) to streamline the ROXAS application file. The settings files are now provided to registered user as part of the installation folder.
- ROXAS main window: added “Manage calibration files” option to open the user's application folder that contains the settings files (*.rsf) to ease management of ROXAS settings.
- ROXAS main window: added “Adjust General ROXAS settings” option to change the default startup settings
- Tree cores, spatial calibration: allow Y origin to be offset >32’768 pixels out of the image. This allows to narrow the specified sector, which improves quality of automatic ring detection.
- New output parameter: replaced previous "Vessel Multiple Fraction" (VMF) by more intuitive "Mean Group Size of Grouped Vessels" (GSGV), defined as (100-VSF)/VMF
- Settings window, Annual ring recognition: added smaller steps in
“Steps of ring border trajectories” to improve accuracy of ring tracing in very long images.
- Advanced Settings window, Miscellaneous: added "Color of
vessel outlines" option
- Bug fixes and general improvements of stability and user friendliness.
5 September 2011 - v1.3.0
- Implemented ROXAS Pro with full functionality vs. ROXAS Basic version without batch processing functionality.
- Added control for parenchyma analysis in ROXAS main window.
- Manual editing: implemented Undo option for the last ring and vessel editing operation.
- Improved output of AOI-based analysis: area-sensitive statistics calculated on AOI area-level in global and annual ring output.
- Improved ROXAS setup file.
- Completely re-structured and extended ROXAS Reference Manual.
- Bug fixes and general improvements of stability and user friendliness.
21 March 2011 - v1.2.0
- Decoupled ROXAS species settings file from compiled version and made it accessible as text-file. The settings files are listed in ROXAS main window > species selection field.
- Added additional options in Advanced window to include all relevant parameters needed for adjusting to a new species.
- Excel output file adjusted to include all relevant parameters in settings tab. Layout is identical to settings text file and may be copy-pasted into a text file to create a new settings file (extension: *.rsf).
- Allow user to define additional AOI’s (besides sector and xylem outline) to which analysis should be limited. In tree cores this may be useful to follow xylem outline (mask around core) or to select tracheid files. Vessels at the AOI borders that may be cut-off are either fully included or excluded depending on there center coordinates. All relevant AOI-level parameters that cannot be easily derived from other statistics are written separately to the output file.
- Improved local contrast enhancement in image processing.
- Added Roxas.ini file which contains easily changeable running options that are not associated with species settings files, e.g. the default species on start-up.
- Bug fixes and general improvements of stability and user friendliness.
8 March 2011 - v1.1.3
- Cross-sections: use trace circumference that are manually drawn by the user as the outmost ring boundary.
- Cross-sections: automatically delete vessels (manually) drawn outside of specified angular sector and very small vessels that are most likely artifacts of manual vessel splitting/drawing.
- Delete vessels outside of outmost ring that may be present due to manual editing or by the small interpolation difference between xylem outline and outmost ring trace.
- New parameter: potential hydraulic conductivity.
- New parameter: vessel grouping index, vessel solitary fraction and vessel multiple fraction (sensu Carlquist 1988/2001)
- Manual editing: allow selecting multiple ring traces to delete in one go.
- Manual editing: new tool to delete several vessels within a user-defined AOI.
- Manual editing: allow multiple vessel tracing in one go.
- Adjusted to Excel 2007 and later: Excel 97-2003 (*.xls) used as default file format.
- Bug fixes and general improvements of stability and user friendliness.
16 January 2010 - v1.1.2
- Created ROXAS installation file including all required ActiveX components and DLL that might not be installed on host machine.
- Adjusted to IPP 6.x: >100’000 objects/vessels can be recognized.
- Several minor bug fixes in batch processing
12 December 2008 - v1.1.0
- Added several control options for the way Analysis should be performed:
- "Tree core(Y) Cross-section (N)", "Consider outline trace in analysis" (only available/relevant in cross-sections!), "Find outline automatically" (only available in cross-sections!); "Only global xylem analysis", "Extended visual output"
- Added a batch spatial calibration functionality.
- Added option to prepare project file for batch running the automatic analysis of several images.
- Added a batch tool for running the automatic analysis of several images.
- Cross-sections: implemented stepwise analysis of sub-regions in large images to prevent
crash in IPP 4.5 when >16,384 objects are found during vessel
extraction.
- Improved vessel extraction algorithm.
- Added button to only update outlines. Give user choice to re-edit after updating (useful in cases where manipulation errors occurred).
- Allow consecutive hitting on junk objects to delete them.
- Added function to split merged vessels.
- Added option to only output essential visual data and not update/draw illustrating images that show Earlywood vessels, Earlywood Border vessels and assignment of vessels to rings.
- Allow to load previously saved annual ring boundaries and vessel outlines accessible for re-editing.
- cross-sections: save and re-use manually drawn xylem outlines
- Generally improved user guidance and information
- Bug fixes and general improvements of stability and user friendliness
12 February 2008 - v1.0.3
- Cross-sections: polar grid laid over source image to ease the selection of the sector to
analyze.
- Tree cores: implemented stepwise analysis of sub-regions in large images to prevent
crash in IPP 4.5 when >16,384 objects are found during vessel
extraction.
- Cross-sections: algorithm to approximate outline trace. The radial
changes in the tangential direction are used to guide algorithms in
“Annual Ring Determination”. This will improve handling of eccentric
roots.
- Added button to allow the user to show/hide the outlines of vessels in
i) “Settings”-window > “Vessel Extraction”-tab and ii) “Manual
Correction”-window. The user can now flip between vessel outlines
on/off, which will ease distinction of wrong and true vessels during
calibration and manual corrections.
- Automatically load the Annotation window when needed in “Manual Editing”.
- Improved writing of data output to Excel. Now 25x faster than before.
- Bug fixes and general improvements for stability and user friendliness.
30 June 2007 - v1.0.0
- First fully functional version with manual editing functionality released.
18 November 2004 - v0.0.7
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