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
Support 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

Prototype finished. See von Arx G & Dietz H. 2005. Automated image analysis of annual rings in the roots of perennial forbs. International Journal of Plant Sciences 166: 723–732 (pdf)

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