Updates history - UU-cellbiology/DoM_Utrecht GitHub Wiki

1.2.5 (2022.11)

  • added import of TrackMate tracks;
  • added "Show Tracks" option;

1.2.4 (2022.10)

  • added Z-range specification for the 3D reconstructions;

1.2.3 (2022.10)

  • fixed local maximum calculation to more strict;

1.2.2 (2021.04)

  • added "intensity threshold" output to Log file;
  • corrected array size (xyOrig) transform allocation for chromatic correction. It would not work/throw exception with images which height is larger than the width (thanks to Klara Jansen/Mithila Burute);
  • for 3D (data with Z) color rendering changed maximum possible intensity value to 99% percentile, to account for possible saturated pixels, thanks to Roderick Tas feedback.

1.2.1 (2020.11)

  • for chromatic correction/calibration made initial image registration optional (in the initial menu). The reason is that in case of very regular spacing grid it detects false shifts;
  • fixed ThunderSTORM import bug, thanks to Oystein Ovrebo feedback.

1.2.0 (2020.08)

  • added option to choose a threshold for detection (measured in SNR);
  • added preview of detected spots in the detection dialog;
  • finished Mavenization of the project;
  • added export/import to ONI Nanoimager format and import from ThunderSTORM;
  • added fix for "Load large RT", since now FIJI sometimes skips first numbering column;
  • original pixel size calculation from Results table during Reconstruction is now rounded to 1 nm;
  • changed the way of histogram calculation for detection of image background and noise (on a convoluted image). Instead of 256 bins by default, it used Freedman-Diaconis rule to calculate optimal bin number. It should help with detection on images that contain some large bright spot (nucleus, etc);
  • for thresholded spots bigger than typical point size, additional search for local maxima inside is included;
  • added Update site;

More feedback from Christophe @cleterrier

  • plots sizes displayed for z-calibration are adjusted depending on the screen resolution;
  • exported data to ThunderSTORM/Fairy Dust is written using dot as decimal separator independently on the locale;

1.1.6 (2018.04)

  • in chromatic correction "warped" channel is MAX projection now, not default;
  • error in SNR estimation is fixed;
  • "Sort Results" function updated to work with regular ResultsTable (which sometimes has 'hidden' columns);
  • Results table precision is now 2 (after floating point), so it should occupy much less space;
  • "Load large Results Table" menu item allows to load, well, large Results Table;
  • "Load Drift Correction" now automatically checks for the file separator (tab or comma);
  • Export/import to MTrackJ is fixed;
  • Main menu is rearranged to have two export/import groups;

Thanks to Christophe @cleterrier following updates were made:

  • average localization precision is now estimated from detections where localization accuracy is less than 1 pixel (before it was only from true positives and caused crash, especially for 3D data),
  • a final number of fitted localizations is now reported to Log file;
  • Z coordinate and localization error averaging is added to the 1 px averaging of photoactivation events;
  • for drift correction, added an option to calculate drift with first batch of frames as a reference (not consecutive). It should work better with smaller drift;
  • added export to ThunderSTORM format;
  • added export to Fairy Dust format for web browser based 3D renderer (viewer is available here);

1.1.5 (2016.09)

  • 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 (2016.09)

  • 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 (2016.08)

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 (2016.08)

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

1.1.1 (2016.08)

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

1.1.0 (2016.08)

  • 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 (2016.07)

  • 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 (2016.07)

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 (2016.07)

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 (2013.05)

  • 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;