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;