[+] Added  
[=] Altered  
[*] Bugfix  

[+] Added UMAP clustering method
[+] Added consensus nucleus outlines and nucleus images to dimensionality reduction plots
[+] Added ability to use dimensionality reduction for display only
[+] Added ability to toggle RGB images in manual clustering
[+] Added ability to set single nucleus image export size and RGB/greyscale
[+] Added ability to save charts to PNG or SVG at standard journal column widths
[+] Added table to nucleus detector showing object sizes and circularities
[=] Improved range of command line arguments
[*] Fixed issue importing .nmd files with merged segments
[*] Fixed issue exporting analysis options

[+] Added ability to create user defined rulesets
[+] Added new XML nmd format to replace binary format
[+] Added bundled user guide
[+] Added Java runtime in downloads
[=] Improved speed of analysis
[=] Improved UI responsiveness for large datasets
[=] Simplified consensus nucleus display
[=] Integrated signal warping into signals tabs
[=] Simplified segment and landmark editing

[+] Added ability to export warped images with dual pseudocolours and consensus outlines
[+] Added ability to open launch configuration file from Edit menu
[=] Revised UI for signal warping
[*] Fixed issue assigning cells to clusters if some cells are not in a cluster
[*] Fixed issue scaling source images opened from individual cells panel
[*] Fixed issue launching when no internet connection is available
[*] Fixed issue with manually assigned tags being lost when datasets are merged

[*] Fixed issue updating dataset source folder in options
[*] Fixed issue fitting prober images to screen size
[*] Fixed issue blending warped signals with arbitary signal colours
[=] Set tag menu items to be coloured in cell segment editing popup

[*] Fixed issue displaying signal colour row at full height in signal overview table
[*] Fix issue copying merged segments to a child dataset created by manual curation

[*] Fixed issue exporting segmented profiles charts when profile length >1000 

[+] Added ability to choose normalised profile length on export
[+] Added ability to import border tag rules from file
[+] Rulesets can be applied on a per-nucleus basis as well as via the median
[=] Replaced rulesets dialog with cleaner UI

[+] Added button to allow profile reversal in individual cells
[*] Fixed mesh view for individual cells when rotated vertically
[*] Fixed issue exporting segmented profiles charts when profile length >1000 

[*] Fixed issue annotating cell borders when image is larger than panel size
[*] Fixed issue displaying profile charts when profile length >1000 

[*] Fixed issue running clustering

[+] Added ability to select nmd save format (standard or XML) to main options (default remains standard)
[+] Added ability to export raw profiles from nuclei
[+] Added ability to export interpolated nucleus outlines
[+] Added ability to export SVG outlines with micron scaling as well as pixel
[=] Log files are now saved to the user home directory by default
[*] Fixed issue displaying image names containing a UUID

[*] Fixed issue calculating hook length and body width

[+] Added ability to mask background for single nucleus export
[+] Added ability to merge signal groups within a dataset
[*] Fixed issue displaying clustering setup with small datasets

[+] Added dimensionality reduction for clustering by t-SNE or PCA
[+] Allow clustering on multiple profiles
[*] Fix segmentation issue when merging datasets with manual segmentation patterns
[*] Fix problem curating new child datasets when blank cell in curation table selected
[=] Improved detection settings and cluster table layout
[=] Combined segment and tag views in the Cells tab

[*] Fix threading on individual cell panels

[*] Fixed issue updating individual cell segments from child datasets

[=] Cluster mapping file does not need all nuclei present; missing nuclei are ignored
[*] Fixed UI update errors

[+] Added multithreading to signal warper
[*] Fixed range overflows in combined warped images
[*] Fixed file paths for signal groups added by workflows

[+] Added ability to check for new version via Help>Check for updates
[+] Added MS-SSIM calculations to signal warper

[*] Fixed image prober settings enabled on creation
[*] Fixed scatter chart display when two datasets have the same name
[*] Fixed misdefinition: aspect ratio renamed to ellipticity

[+] Workflows defined by xml files  
[+] Shell analysis comparison of multiple datasets  
[+] Dockable UI  
[+] FISH signal counts chart and filtering  
[+] Filtering of cells based on shell results  
[=] Segmentation uses a new method for segment fitting  
[=] Shell analysis random distributions are calculated from cells, not estimated  
[=] Workspace file format changed to xml to include metadata  
[*] Signal angles calculated correctly  

[+] Refold override added to global options  
[+] Dataset names in consensus nucleus SVG exports  
[+] Ability to refold multiple consensus nuclei at once  
[+] Image folder name included as column in dataset stats export  
[+] Workspaces displayed in populations panel  
[+] Coefficient of variability to nuclear stats table  
[+] Ability to change image source folder from Images tab  
[=] Better detection and alerting of old version numbers  
[=] Shell analysis random testing is limited to 100,000 pixels  
[=] Performance improvements with >10000 cells  
[*] Random sampling updated to new analysis method  
[*] Drag and drop of workspaces works on log panel  
[*] Hook length calculation for stubby nuclei  
[*] Crescent moon consensus for round nuclei  
[*] 'Copy from dataset' analysis setup does not replace folder selection  
[*] Merge sources can be highlighted in the cluster tree viewer  

[+] Tree selection of signal groups in signal warper  
[+] Colocalisation visualisation in signal warper  
[+] Shells tab can show shells overlaid on nuclei  
[+] Memory and task monitors  
[=] Images tab can show multiple datasets  
[*] Merges of merges now remember all merge sources  
[*] Signal visibility toggle now affects shells tab  
[*] Wilcoxon tests use pixel or micron as set in global options  

[+] Multiple signal groups displayed in signal warper  
[+] Validation of dataset segmentation on dataset load  
[=] Image probers have grey background to make image boundaries clearer  
[*] Bug copying segments to curated collections  
[*] Bug calculating segment stats  

[=] **Program requires libraries MorphoLibJ and JFreeSVG

- these are included in the complete install file  
[+] Profile samples added to stats export  
[+] Images tab to show all cells annotated in an analysed image  
[+] Ability to export SVG of consensus nucleus  
[=] Profile refolder uses median points for non-lobed cells rather than best-fit nucleus .Can be overridden in config file options  
[=] Image prober does not display irrelevant filters  
[*] Bug calculating bounding rectangle of vertical nuclei  
[*] Bug converting old dataset versions  

[+] Combined analysis setup and image prober  
[+] Consensus nucleus with shells overlaid in shells panel  
[+] Signals>Colocalisation tab to show distances between closest signal pairs between channels  
[+] Ability to export dataset statistics for external analysis (Right click dataset(s)>Export stats)  
[+] Total number of selected cells are shown in dataset table header  
[+] Config file for global options and default analysis parameters  
[+] Program error log file in jar directory  
[=] Reordered tabs to separate cell versus nucleus data  
[=] Improved speed of signal warping  
[*] Correct export of shell bar chart data  
[*] Consensus nucleus refolds correctly  

[+] Charts and tables load in background to reduce UI freezing with large datasets.  
[+] Workspaces to allow multiple nmd files to be reopened in one go.  
[+] Ability to choose chart dataset order by Ctrl-clicking in populations panel  
[+] Ability to set missing border tags via the border tag editing panel without using the Ruleset dialog  
[=] Improved memory efficiency of the program  
[=] Ruleset dialog displays cumulative effect of rules  
[=] Shell analysis can be re-run at will.  
[=] If a consensus nucleus is present, a simulated random shell result is calculated  
[=] Pairwise Venn table has dataset colours  
[=] Pig sperm reference point detection ruleset changed to be more robust.  
[=] Segments cannot be split or merged for child datasets; changes must be made to the root dataset  
[*] New cluster group numbering corrected  

[+] Ruleset dialog to visualise rules used to identify points in a profile, change existing rules, and create new rules  
[+] Ability to create custom BorderTags via the Ruleset dialog  
[+] Violin plots to optionally replace boxplots (toggle via main options)  
[+] Ability to cluster based on profiles of all types, not just angle profiles  
[+] Ability to cluster based on nucleus mesh face sizes  
[+] Program warns on exit if datasets have changed since last save  
[+] Dialog for cell complete resegmentation  
[+] Loading bars to ImageProber windows  
[=] Cluster groups show in populations tree  
[=] Clustering options are greyed out when false or N/A in clusters tab  
[=] Hidden the control panel in  cluster tree viewer  
[=] Replaced cell curation interface to allow looking over of the entire dataset  
[=] Drag-and-drop to open nmd files works across entire interface  
[=] Drag-and-drop of folders will begin a new analysis  
[*] Variability not displaying in scatter plots  
[*] Merged datasets with the same cells from different analyses not displaying in tree viewer  
[*] Signal warper hanging when comparison meshes cannot be created  

[+] Ability to open nmd file by drag-and-drop onto populations panel  
[+] Mean and standard error of the mean to nucleus stats table  
[=] Cell component selection is maintained when cells changed in the cell detail tab  
[=] 'Change scale' and 'Show source image' actions moved from cell info table into buttons  
[=] Redundant options removed from populations popup menu  
[=] Measurement scale (pixels or microns) moved to a global option in the top panel, rather than per chart  
[*] Bounding rectangles not recached on top and bottom vertical point change  
[*] Signal warper cell counter now counts properly  
[*] Consensus nucleus scale is now updated with individual cells  

[+] Ability to copy analysis options from an open dataset when running a new analysis  
[+] Ability to change border tags in the population via Editing>Border tags tab  
[+] Border tags can be set on individual cells via the Editing>Cells tab  
[+] Rulesets for identifying features in a profile 
[+] Nucleus mesh has faces as well as edges  
[+] Nucleus mesh comparisons to consensus in Cells tab  
[+] Warp image to match consensus in cells tab  
[+] Warp nuclear signal images onto a consensus nucleus in Signals overview tab  
[+] Scatter plots for Nucleus Statistics and Signal Statistics  
[+] Option to reverse nucleus profiles via Editing>Cells>Segments tab  
[=] Angle profiles are calculated with a window size proportional to perimeter, not fixed  
[=] Vertical nucleus and head/hook calculations occur on dataset load, rather than first chart caching  
[=] Signal groups are identified by a unique id  
[=] Cells tab has sub-tabs to allow better view of profiles and tables  
[=] Log panel wraps lines to fit horizontal space  
[=] 'Average stats' tab moved to Nucleus stats tab from Analysis info  
[=] Segments editing tab has range chart and detailed point-by-point chart  
[=] Logging levels include FINER  
[=] Images are no longer exported by default  
[=] Scales are in pixels/micron, not microns/pixel by default  
[=] FISH remapping nucleus highlights changed to solid fills  
[*] Signal angle boxplots not taking an accurate median when signals cross 359-0 angle boundary  
[*] ImageProber full scale images had non-functional Yes and No buttons - buttons removed  
[*] ImageProber shows signal channels when appropriate  
[*] Profile charts now have auto-range on y-axis for profile types that are not angles  
[*] Histogram bin size selection does not produce empty bins in integer-stepped datasets  
[*] Bug calculating hook lengths and body widths in rodent sperm  

[+] Overlay of vertically oriented nucleus outlines aligned by centre of mass in 'Nuclear charts':'Overlays' tab  
[+] Segment start positions annotated against consensus nuclei in 'Segments':'Start positions' tab  
[+] Comparison of consensus nucleus meshes  
[+] Splash screen to cover long loading times  
[*] Morpological closing occasionally failed to close single pixel gaps  
[*] Orientation point not assigned to a segment boundary if median profiles have no obvious features  
[*] Program does not warn if Java version is incorrect  
[*] Analysis options not displaying for merged datasets when equal  

[=] **Program requires Java version >=1.8

[=] Moved Mann-Whitney nuclear tests to the Nuclear boxplots panel from Inter-dataset comparisons tab  
[=] Speed improvements in single-threaded segmentation  
[=] Analysis setup options no longer has refold modes - fast is set as default  
[+] Program can use multiple threads for nucleus detection and segmentation  
[+] segment length Mann-Whitney U-tests in Segments panel  
[+] Use segment lengths as clustering or tree-building parameters  
[+] Highlighting of identical analysis setup options across datasets in Nucleus detection tab  
[+] Pairwise magnitude tab in Nucleus charts tab and segments tab  
[+] random sampling of populations to assess significance of sub-population magnitude differences  
[+] data export from charts via right-click menu  
[+] analysis setup option to keep 'failed' nuclei as a separate round cell population  
[+] Testing of angle profile window size changes to a dataset  
[+] all profile types are represented in the profiles and cells tabs  
[+] Ability to perform Kruskal-Wallis tests on franken-normalised median profiles.  
[+] Ability to generate child datasets based on an imported list of cells  
[*] FISH remapping panel header and cancel button text was showing default ImageProber heading text  
[*] Hook and hump assignment was occasionally incorrect for new analyses of rodent sperm  
[*] Background images in cells tab render above the segmented outline  
[*] Segmentation problems with large nuclei  
[*] Populations panel folders expand when panel updates  
[*] Copy button missing from consensus nucleus chart right click menu  

[+] Export the cells in a dataset to allow clusters and curated groups to be imported in future versions  

[=] clustering options dialog reordered for clarity; better customisation of clustering variables  
[=] Comparisons between datasets (Venn, Wilcoxon, Kruskal) have been moved to a single tab, called 'Inter-dataset comparisons'  
[=] The Venn and pairwise Venn tables have been split to separate tabs  
[=] Tabs that allow modification of data have been placed in a new tab called 'Editing'. These are 'Cells' and 'Segmentation'  
[=] Program options are combined into one window  
[+] Kruskal-Wallis comparison of dataset profiles  
[+] Manual cell curator, to remove poorly detected nuclei  
[+] Annotated source image display from Cells tab  
[+] Draggable segment boundary markers to the nucleus profile in the Cells tab, and the median profile in the 'Segmentation' tab  
[+] Cluster group creation for manual clusters  
[+] nucleus tree individual cluster or cluster group highlighting via dropdown menu  
[+] nucleus tree builder without clustering  
[+] tables can be exported to tab-separated text file via right-click menu  
[+] new nucleus statistics - [all] angle between reference and orientation point, [mouse sperm] hook length, body width  
[+] dataset boolean operations  
[+] segment splitting  
[+] Alignment of mouse sperm by the flat region below the hook, and rotation option in the Cells tab  
[+] Ability to update signal source file paths from Signals overview tab  
[*] image paths not recognised when datasets are moved between computers  
[*] log file not being written after initial profiling  
[*] Mouse sperm hook and hump sides mis-assigned causing signal angles to calculate incorrectly  

[=] aspect ratio nuclear stat; uses bounding box height / width, replaces feret / min diameter  
[=] Image Prober to display greyscale images  
[+] confidence intervals about the mean to nuclear statistics tab  
[+] scaling factors for 'full scale' images in title bar in Image Prober  
[+] multi-dataset stats table in segments tab  
[+] histograms and density plots in segments tab  
[+] border tag update when segment boundaries changed in individual nuclei  
[+] newick tree viewer for hierarchical clusters  
[+] manual clustering based on hierarchical tree  
[+] clustering by similarity matrix, as alternative to area, circularity, aspect  
[*] MacOS resource fork files analysed as images in Windows  
[*] bug in pig segmentation (reference point not at tail)  
[*] histogram display bug  
[*] bug displaying null data when errors occur in segments tab  

[+] bounding box measures to nuclear statistics  
[+] pairwise table to Venn tab  
[+] option to re-refold consensus nuclei  
[+] cross-profile dip-test p-value chart to modality panel  
[+] confirm dialog to collection filtering using histograms  
[*] bug in swatch selection  
[*] bug in cell duplication across clusters  
[*] bug in cluster group numbering  

[+] image prober for nuclear signal detection  
[+] new logging system 
[+] caching of some charts to improve speed with large datasets  
[*] bug in colouring of histogram datasets  
[*] bug in duplicate checking of new dataset names  
[*] bug in consensus refolding  
[*] bug in deleting clusters  

[+] images showing the process of nucleus detection to the image prober  
[*] bug in chromocentre flattening  
[*] bug in morphological closing  

[+] ability to merge and unmerge segments  
* Reworked segments display panel for better display of multiple datasets  
[+] micron/pixel display option to charts based on scale set for each cell  
[+] unimodality testing via Hartigan's Dip Test on profile values to the 'Variability'  profile panel  
[+] 'Modality' panel to Profiles panel to display the range of values in the profile at each point  
[+] unimodality testing for nuclear statistics to 'Analysis info' tab  
[+] unimodality testing for segment lengths to 'Segments' stats table  
[+] probability density function to histograms for mode estimation  
[+] manual population filtering from the histograms panel  
* Split clusters and merges to separate tabs for future expansion  
* Allowed multiple clusterings for a dataset; results are stored as cluster groups  
[=] the clustering setup options interface for clarity and future expansion  
[+] external required plugin check on launch  
[*] bugs in segmentation assignment  

[+] ability to merge segments  
[+] multi-dataset view to segment boxplot panel  
[+] segment colouring options via 'Set swatch' option in top panel  
[+] toggle-able display of border tags in profiles  
[+] optional Kuwahara filter in analysis setup  
[+] optional chromocentre flattening in analysis setup  
[+] preview of nuclei detected with analysis options before committing to full analysis  
[*] to consensus panel rendering in multi-dataset view  

[*] Various bug fixes. 
[*] Improved merging of datasets. 
[+] circularity and aspect ratio charts. 
[*] aspect of cell chart.  

[+] Replaced the segment fitter with a more robust version.  
[=] Improvements to the charting.  
[+] ability to read 16 bit greyscale images  

* 1.9.2 Fixes numerous bugs and moves display code for future expansion.  
* 1.9.1 Migrated new analysis to progressable.  
* 1.9.0 Overhaul to allow sperm tail detection and reverse signal detection. UI rearranged.  
* 1.8.1 Numerous bugfixes. Not given out; frozen in favour of 1.9.0  
* 1.8.0 Graphical interface added  
* 1.7.0 Converted to module style. Segmentation of nuclei, basic cluster reprofiling within analysis session.  
* 1.6.2 Added full chi square abillity to shell analysis and fixed Nucleus Detector bug  
* 1.6.1 IQR added to consensus nucleus border. Reanalysis images are individually aligned. Greyscale images converted to RGB. Shell analysis.  
* 1.6.0 Major refactor to add index based profiling and sliding window fitting.  
* 1.5.0 Added a GUI for analysis settings.  
* 1.4.1 All three plugins added to one jar: Nuclear_Analysis.jar  
* 1.4.0 Restructured into separate classes. This version sent to Kent for pig analysis  
* 1.3.0 Internal only  
* 1.2.0 Internal only  
* 1.1.0 Internal only  
* 1.0.0 First working version. Used for demo at Kent and first pass analysis