The Acquiarium software is continuously being developed since 2005. This page shortly describes changes since the first version was released in November 2007.

We list only the most important changes and the new features of every publically available Acquirium release.

June 12, 2012, release

• Mapping module settings are saved to configuration file.
• Smart intensity stretch function added.
• Behaves better on read only depositories.
  
• New segmentation plugin (dynamic thresholding based on user specified number of objects that should appear in the final segmentation)
  

August 26, 2011, release

• VOI export plugin improved.
• Fixed VOI list redraw problems when modal dialog was opened.

August 22, 2011, release

• New plugin for VOI export.
  
• GUI improvements (3D viewer, navigation in AF viewer).
• Changes to retain compatibility with the latest version of the Huygens software
  
• Code improvements (bug fixes, optimizations for speed).

February 11, 2010, release

• Automatic shift correction improved.
  
• Support for combo ZDrive controls implemented (e.g. Piezo + Microscope body). 
• Bug fixes (EMAX plug-in, registration module).
• Deconvolution implemented as a plugin.
  

December 4, 2009, release

• Deconvolution manager added.
• Drivers: Prior Proscan controller driver implemented, Zeiss MTB and Andor drivers updated
  
• New plugin performing spot segmentation based on the h-dome transformation.
  
• Measurements plug-in completely reworked. Measured parameters are linked to objects (dynamic solution). 
• VOIs can be tagged by a string. The tag is saved in depository and can be displayed in VOI browser as a new column. Import plugin put the original filename here.
• It is possible to select and delete multiple objects using left mouse button and shift key
  
• Fixed problems with loading objects.txt from paths containing letters with diacritics
• GUI improvements and bug fixes.
  

July 22, 2009

The work on tutorials was started.

July 1, 2009

• Acquiarium was presented at ISBI conference in Boston, USA. You can download the ISBI poster.
  

June 30, 2009, release (version presented at ISBI in Boston, USA)

• Object parameters are handled in dynamic way.

• Graph selectors (histogram, scatter diagram)
  
• Batch processing of plug-ins
  
• New plug-ins (FISH dot counting, PML bodies analysis - experimental version)
  
• GUI improvments and bug fixes
  

April 20, 2009, release (version presented at FOM in Krakow, Poland)

• ROIs renamed to VOIs in order to emphasize their volume nature.
• Nine recent depositories are remembered in File menu.
• Expected finish time is being estimated by scanning modes.
• The range in spin controls for setting a size of automatically found boxes was widened.
• Segmentation log can be opened directly from Object inspector.
  
• Browsers:
  • Filter is applied immediately after its definition. It is no loger needed to click on use filter button later.
    
  • VOI browseris automatically reloaded after plugin execution.
    
  • Improved consistency between browsers.
  • Columns for user params added in object browser.
  • Browsers state is saved in configuration file.
  • Reload icon added on toolbar.
  • Object browsers can load objects from selected groups only.
  • Better column formating in some columns.
  • User can let automatically adjust column widths.
  • Coordinate id is displayed in coordinate lists.
    
• Plug-ins
  • New plug-in computing expected intensity in sub-domains of an object added.
  • New plug-in computing intensity distribution within groups.
  • Automatic shift plug-in improved.
  • Hysteresis thresholding plug-in enhanced (better dialog, code optimization).
  • Small dot segmentation (3D) plug-in according to Kozubek et. al. implemented.  
  • All VOI manipulation plug-ins put together in one sub-menu.
  • Many plug-ins rewritten in order to allow batch execution of plug-ins without a user interaction in future. 
• Bug fixes (e.g., changing of column width in browsers, exception handling in plug-ins, cropping, deleting of damaged VOIs, ...)

April 6, 2009

• Acquiarium was presented at Focus on Microscopy conference on Monday, April 6 in Krakow, Poland.

March 11, 2009, release:

• Image correction part significantly improved.
• Batch of 3D images can be displayed.
• Gallery of slices can be generated and saved into a file (available in windows displaying orthogonal cross sections).
• Plug-ins can be started directly from VOI/ROI browser (selected items are passed to the plug-in for further processing).
• Fast point-based 3D alignment plug-in was made more robust and its GUI was improved.
• New plug-ins added (ROI manipulation, five segmentation plug-ins added, see Acquiarium plug-ins for complete list).
• Image preprocessing and postprocessing tabs were introduced into segmentation dialogs.
• FOVs and ROIs/VOIs can be renumbered and exported into an another depository.
  
• GUI improvements (e.g. more parameters are remembered in dialogs, browsers remember their states, several short-cut keys added, menus slightly reorganized)
• Code bug fixes and optimizations.

February 2, 2009, release (version 1.6):

• The list of images that are stored in depository can be displayed and manipulated in new browsers. Two image list browsers added: (1) raw data browser (2) ROI browser (it will be renamed to VOI browser soon). They show a thumbnail image and the important parameters for each image in
  a depository. One can sort or filter the list, delete items, or select items for processing (e.g., image correction, image analysis, visualization in other windows, etc.)
• Object browser added. The object browser shows a table of objects where each row belongs to one object and the columns contain objects’ attributes. One can perform usual table operations (e.g., sorting, filtering, deleting, etc.). The object browser is interconnected with VOI browser. It means one can simply select subset of VOIs containing objects of interest.
• Fast point-based 3D alignment of live cells plug-in included.
• Image import plug-in improved.
• Exposure time selection box can be linked with binning selection in Acq. frame.
• Chromatic abberation code improved.
• Automatic finding of crop-boxes added.
  
• Automatic chromatic shift correction (based on mutual information registration) added.
  
• Preprocessing and postprocessing steps added in many plug-ins.

December 18, 2008, release:

• New channels can be defined by pressing 'I' key instead of INSERT key in channel list dialog.
  
• OK button is set as focused in Open depository dialog. It means that the sequence 'Ctrl+O', 'Enter' leads to the fast openning of the most recent depository.
• New segmentation plugins developed (they implements FISH signal and nucleus detection algorithms by [Netten et. al. 1997] and [Gue et. al. 2005]).
• Plugins are alphabetically sorted in menu.

December 3, 2008, release:

• Small bug in parent group computation fixed.
• Database communication improved in chromatic aberation correction procedure.
  
• Stage coordinates can be simply set by pressing ENTER key in HW control window.
• FISH2.0 import plugin set correct date and time (needed by chromatic aberation correction procedure).
• Information about images is dispalyed in maximum intensity projection (AF) viewer in status bar.
• Cliping plane rotation significantly improved in 3D volume visualization window.

October 29, 2008, release:

• GUI improvements and bug fixes.
• Chromatic aberration corrections integrated.
• Acquisition modes implemented dynamicaly (dynamic acquisition modes).
• Surface of segmented objects can be rendered in volume visualisation window.
• Option for deleting ROIs and channels (from both FOVs and ROIs) added. Deleting groups reworked.
  
• Maximum projection (AF) images are saved into the ICS file format.
• Software preferences are saved in user space instead of global space. Each user can have his/her own preferences.
  
• Meander scanning mode updated.
• New acquisition mode for fast 2D acquisition of living cells implemented.
  
• 16-bit non-EM Andor camera driver added.
• Zeiss MTB 2004 driver enhanced (lightpath selection, displaying of camera port)
• AA Opto-Electronic AOTF device driver initialization made more robust
• FISH 2.0 import plugin improved.

September 16, 2008, release:

• GUI improvements and bug fixes
• Volume visualisation window created.
• Software internaly works with images as they were 16-bit (8-bit branch was terminated).

• Drivers for Zeiss MTB 2.50 compatible microscopes developed and added.
• Andor and PVCAM camera drivers improved.
• AA Opto-Electronic AOTF device driver improved (user can set filter power)
• Scanning modes improved (e.g. user can define overlap in meander scanning or a delay after filter exchange can be defined in a config file).

July 11, 2008, release:

• GUI improvements and bug fixes.
• Help and documentation significantly improved.
• Software turned to the newest wxWidgets (version 2.8).
  
• Software turned to dynamic version supporting dynamic plugins and dynamic drivers.
  
• Added new import option - import of individual files. User can select a directory and all images (ics, tga, tif, jpg, LOCI BioFormats) in that directory will be imported as separate ROI positions. Images of GRAY8, GRAY16, float, RGB8 and RGB16 types can be imported.
  
• Added new type of total file. It collects the volume and surface for all objects in selected groups together. The number of objects in groups is also contained.
  
• An user can select reference points for local radius computation.
• Thresolding algorithms can run in space given by parent mask only.
• New algorithm for computing and exporting local intensity characteristics.
• Collocaliation plugin developed.
  
• New methods for automatic threshold selection added.
• IsoData method added to hysteresis thresholding dialog.
  
• Detailed processing and scanning logs can be opened directly from the software.
  

• Leica filter driver added.
• AA Opto-Electronic AOTF device driver added.
• Andor and PVCAM camera drivers modified.
• Enhanced dummy hardware driver added.
  
• Stage|camera image orientation can be specified in a config file.
• Improvements in Zeiss drivers (right sideport control enabled).
  
• Improvement of information tracking about data acquisition hardware used.
  

Version 1.0: released in November 2007.

The version is described in the article Acquiarium version 1.0.