Updates history

1.1.6 (coming soon)

• in chromatic correction "warped" channel is MAX projection now, not default;

1.1.5

• error for borders of scaled z colorscale fixed;
• added output of reference points for color correction to results table option;
• drift correction is FFT based now, no limit on maximum displacement between windows;
• error for Y_(px) calculation in 'table' mode for color correction is fixed;

1.1.4

• added chromatic aberration (color) correction. Needs some testing, when done, gonna be major update;
• zmin and zmax are taken from the Results table, not from stored calibration;

1.1.3

extensive testing by Christophe @cleterrier lead to:

• fixing 1/2 pixel shift in reporting X and Y localizations;
• error for translation/average photoactivation rendering sequence;
• particle detection with SD ~ 1 pixel efficiency;

1.1.2

• added calculation of Z-axis localization error;
• for Z-stack reconstruction points are rendered as 3D Gaussians (normalized);

1.1.1

• added accounting for X and Y "wobbling" in Z calibration;
• added "save", "load" and "show" options for Z calibration;

1.1.0

• added colorcoded rendering of Z-stacks (max proj and average color);
• it is accompanied by colorbar showing colorcode;
• added multiple LUTS loaded from FIJI/ImageJ;
• added "Scaled colorcode for depth" option that stretches LUTs according to Z particles distribution;
• fixed duplicate fields names to enable call of "Reconstruct Image" from macro;

1.0.2

• Z-calibration dialog is almost completely re-written;
• parameters as polynomial degree, zero position and range added to dialog and can be changed;
• the dialog now works interactively in "non-modal" mode.

1.0.1

first addition of 3D astigmatism data processing:

• added dialog for z-calibration creation and fitting;
• added rendering of 3D data that only supports "Z-stack" option.

1.0.0

first release! many internal and external changes:

• sequence of columns is changed in Results table (reason for version increase), new columns added (errors for SDX,SDY,etc), chi_square is now Rsquared of fit;
• almost all results now in nm units, not pixels! (localization error, SD, etc) check new columns titles;
• the same happened with dialogues, most parameters now in nm (apart from SD of PSF, still in pixels for convenience);
• added detailed and extensive logging for all analysis/reconstruction parameters displayed in ImageJ Log window. Good for keeping tabs;
• "average consecutive localizations" in "Reconstruct" menu now can update results table with new weighted values from averaging;
• final render of "Reconstruct Image" now is in 32-bit mode. Meaning that each particle integrated intensity is equal exactly to 1, i.e. total integrated intensity of image is equal to total number of particles;
• fitting speed is increased even more by adding additional constrain for convergence (error relative increase);
• if ROI is selected before "Detect Particles" start, plugin will report/show only particle inside this ROI;
• Drift correction is now a separate menu item;
• Shift between intermediate reconstructions in Drift Correction now in nm too;
• Drift correction cross-correlation calculation is now normalized and some minor boundary issues are fixed;
• new option to specify pixel size Drift correction intermediate reconstructions (before it was always with average localization precision), it should increase speed of Drift correction;
• in Drift Correction render options of intermediate reconstructions are picked up from the last call of "Reconstruct" function and displayed in parameters window;
• Drift correction results now can by applied to Results table;
• Drift correction results can be saved and later loaded and applied to Results table;
• GPU is temporarily disabled to update for new format Results table later;
• minor bug in calculation of Integrated Intensity is fixed;
• minor bug in Reconstruction is fixed (precision round -> ceil);
• Load Particles and Save Particles functions are re-written for reverse compatibility with previous versions;

0.9.2

• major revision by Jalmar and Jens, implementing GPU support

0.2.4

• added automatic image width and height estimation (max X and Y) in the Reconstruction;
• fixed exception handling during fitting (error with inverse matrix). Some detected spots occasionally were lost because of it;
• fixed some names in the Reconstruction dialog (again). Still this version should be compatible with script;
• in Results table generated after linking I've substituted column 'mark last detections' for 'reverse number of a particle in track' column. It seems to be much more general and universal solution;
• fixed displaying particles at 'Linking'. Now particles could be shown separately without tracks (before it was only together).

0.2.3

• another fix in linking of tracks, now indeed the closest detected particle is used (Eugene);
• another fix in names of fields in "Reconstruction" module (Bas).

0.2.0

• fixed names of fields and interface of the "Reconstruction" module. Now it is possible to call it correctly from a macro;
• fixed linking of tracks, especially frame's gaps handling;
• added export of tracks to MTrackJ;