Fluorescence microscopy image analysis
automation - time series - physiology

Version history:
2.0.15beta (06.05.2009) First release
2.0.16beta (06.15.2009) More help/hints added, fixed typos
2.0.18beta (06.29.2009) bugfixes, improved consistency in appearance/language, online help added
2.0.25beta (10.29.2009) Several new functions: Advanced segmentation and thresholding, faster and more versatile ND2 file reading, more versatile LSM file loading, RGB TIF loading, 32bit TIF loading,  Wiener filtering, Anisotropic diffusion filtering, Mean calculation in Plot Windows, Image arithmetic with single frames, smoother toolbar operation, and lots of bufgixes...
2.0.27beta (11.11.2009) Improved histogram interpolation, Added block mode for Optical Flow, and new functions: Temporal Block filter, New Time Scale, Mask Images, Fill Mask, Strip to Well Count. Bugfixes and updated help
2.0.29beta (12.02.2009) Added blind spectral unmixing with nonnegative matrix factorization. Various bugfixes, improved plotting of intensities corresponding to segments. Fixed logarithm calculation.
2.0.36beta (02.03.2010) Object tracking, Cell death & division counting algorithms added, various bugfixes
2.0.38beta (03.07.2010) Threshold has new parameter 'Keep orignal mask', Align Channels has new parameter 'Transform all linked images', various bufgixes
2.0.53beta (01.13.2011) Improvement of existing file format readers, new Bio-formats reader interface. Excel Data Window and spreadsheet output of analysis functions. PlotCorrelation function. Segmentation of more than 65334 objects. Reference images and more versatile image background subtraction. Optical Density calculation for brightfield images Bugfixes and updated help.
2.1.3 (02.10.2012) Improved Windows 7 compatibility (Java/Bio- formats, drag-and-drop, default folders fixed)
New features: Histogram reference image. More versatile and new background subtraction methods: Mean and Median of pixels below percentile of max projected image (for taking the background over the same pixels  for the whole time lapse). Fiber Length and Breadth as well as intensity informations can be used as Segmentation Classifiers now. Handling multiwell plate well names. Plate output for plotting functions when outputting to Excel window. Improved Excel window and xlsx file saving. Full size RGB export, JPG export.
10 new functions: Advanced Segmentation Sep.Seed (for e.g. segementing cell cultures based on nuclear markers), Reevaluate Segments, Link Image Windows (available in macro now), Set Reference Image (available in macro now), Wait for all inputs (for macro flow control), Remove Blank Frames, Mask Borders and 2D DFT Filter Butterworth BP Tiled (for working with tiled images), Detect Nuclei Convolution (for detect nuclei appearing as empty holes), Set Segmentation Intensity Classifiers (intensity information in linked images can be used now as segmentation classifiers).
Speed-optimizations in many functions...
Bugfixes: odd pixel width AVI files, Median filters  work with masks now, Percentile calculation in masked images works now in all cases. Further bugfixes...
Optimizations: decreased memory usage during segmentation
Note:  2DDFT filter cut on and off values are properly scaled now when using Enlarge Paper or Protect Edges options and units as pixels. Saved *.ips files accommodate this change automatically. In most cases old values (created between 2.025 and this version) have to be halved if these options were used.
2.2.0 (12.03.12) New features: Zoom and pan image windows, Internal reader is compatible now with NIS Elements 4 nd2 files, Tiled image registration functions. Plot Tracking Parameters (velocities or distance traveled). Spherical aberration correction (to be documented). Full size RGB image (avi or jpg) export.
Bugfixes: trial period works now properly. some cases of crashes upon deleting ROIs / closing image windows or resizing plots resolved.
Changes: added columns at Excel Data Window output for Plot and Count colocalization functions for a uniform output.
2.3.4 (08.17.2013) New features: Mitochondrial membrane potential calibration wizard - beta
2.3.8 (01.29.2014) New features: Synchronized frame scrolling of linked image windows. More membrane potential calibration algorithms and error propagation. Mean calculation in plots.
Improvements:
Mitochondrial membrane potential calibration wizard, nicer axes tick labels. Improved error handling. More versatile marks for means handling on plots.
Bugfixes: Fixed nd2 loading of lambda-only ND acquisition. 
2.4.0 (03/21/2014) VisualMacro was renamed to VisualPipeline to better describe its functionality.
Improved:
Multi Dimensional Open dialogs can be reactivated to be used with VisualPipelines. Plots automatically switch to "traces only" mode when showing larger amount of data. Bio-Formats was upgraded to 5.0.0. Improved help and documentation pages.
Bugfixes:
Fixed loading of Metamorph files that are not stored in sequential order. VisualPipeline color scheme can accommodate now to black background. Mean of all traces DF/F0 plotting infinite cycle fixed. Tiled Image Stabilizer fixed. Fixes in plasma membrane potential calibrations. In some cases image opening in the background resulted locked-up Image Windows. This is fixed now.
2.5.0 (08/19/2014)

New functions: Template Matching to retrieve regions of images based on similarity; Correct Intensity Jumps to fix illumination artifacts; Z-drift Correction; Weighted Z-projection. Excel window automation in pipelines. Calculation, copying and saving error bars for mean traces. Scalar arithmetic can be constrained to specified frames of a time lapse.
Improved functions: Blind spectral unmixing: a lot improved convergence, and additional features e.g. fixed coefficients for known crossbleed. Image registration functions run now even faster than before. Improved multi-dimensional file opening with bio-formats. The internal lsm reader was re-optimized for loading large files. Membrane potential calibration wizard.

3.0.0 (07/13/2015) Major changes: Pipelines are integrated similarly to image processing functions into the main menu and main property bar. Pipelines can be executed on single or multiple positions, including whole microplates from the main menu and toolbar and from Multi-Dimensional open dialog. Pipelines can have their own parameters that control functions within the pipeline. Pipelines (*.ips) are saved now into an XML-based file format, but all previously created pipeline (macro) files are compatible with this and future versions of Image Analyst MKII. The new format also offers forward compatibility in the future.
A collection of 75 generic pipelines and specific biologic applications are included.
A search function allows to find functions and pipelines quickly. Numeric function parameters can evaluate mathematical expressions.
New functions: Completed Membrane Potential Calibration Wizard with supporting pipelines to prepare images for potentiometric calibration, and mitochondria:cell volume fractionator pipelines to process confocal microscopic serologic data. Temporal Rolling Projection. Create ROIs from Segments. Intensity-based ROI Classifiers. Segmentation-based automatic ROI drawing (pipeline). Copy ROIs between images.  
Improved functions:
Data transfer to Excel was speeded up. More options to organize Multi-Dimensional data output to Excel in Plot functions. All Plot functions have new options for normalization, mean, median and rate calculation. Standard error calculation for means of traces. Robust pipeline stopping and resetting. Larger variety of LUTs. Improved automatic ROI drawing.  Default folders and the default loader can be specified from menu. Improved file name parsing for automation. Numerous bugfixes and improved overall stability.
3.1.0 (11/08/2015) Improved functions: Optimized for Windows 8 and 10. Speed increments by increased parallelization. Smoother handling of input focus. Help buttons were added to major dialogs.
New functions (or function options): Repeated template matching on image series. High pass, band pass, Long Pass filter optimizer in the Set DFT Filter dialog. Improved z-drift correction in the Multi-dimensional open dialog.
 "Dilated mask" versions of the "Mean" and "Median of pixels below percentile of max projection" background subtraction algorithm. "Range of channel numbers to lay out" parameter in plotting functions.
Minor bugfixes to ensure stability, smooth operation and consistency of handling.
3.2.0 (3/28/2016)
  • New functions:
    • High DPI and 4K display support, support of differing scaling between displays
    • TIFF folder open: flexible open method for folders with many TIFF files or multi-dimensional data sets organized into folders of many TIFF files
    • Opening of BD Pathway recordings
    • Measurement of distance of segments from ROI (Plot type:'Each') or from other segments (Distance from Segments function)
  • Improved functions:
    • Improved Excel Data Window behavior
    • Improvements in opening AVI files
    • Opening Metafluor files with numbers only extensions
    • File creation time is used to establish time axis if TIFF metadata is missing
    • Smarter detection of well names in position names (for all file types)
  • Other changes:
    • 23 other minor improvements or fixes