Updates history

0.5.5

• previously in the case of zero detected particles, "append" Summary table function would reset the table, now it appends zero detections, thanks to Giel Korsten feedback.

0.5.4

• added extra columns to "Summary" Table corresponding to the case where all channels colocalize (with channel 1 as a reference, see updated description for details);

0.5.3

• added an option to "Reset" or "Append" new results in the "Summary" table.

0.5.2

• in case of "no particles detected", plugin now generates an empty Results table and does not show anymore the window with a message. It should be better for batch/macro running mode (suggested by Christian Bates);
• fixed small bug with preview of detections;
• added an option of "Add non-colocalized particles" to ROI manager (suggested by Sonny Panichnantakul).

0.5.1

• fixed "frames/slices" jumping during preview, now detection is previewed only on the frame/slice that is selected before the start of plugin;
• in threshold calculation/gaussian histogram fitting removal of the peak substituted to its smoothing.

0.5.0

Major update.

• plugin now works with more than 2 color channels;
• added option to choose between "Ovals" and "Rectangles" ROI shapes;
• Results table format changed.

0.4.2

• changed "Summary" table to ResultsTable class, to be accessible from jython (from this thread);

0.4.1

• fixed the issue with intensity estimationfor colocalized particles (see previous update). Now if particle 1 from channel 1 is colocalized with particle 2 from channel 2, plugin makes a rectangular ROI that includes both corresponding particle ROIs and recalculates intensities for both particles in both channels. Now it does not matter, intensity data from which channel was taked for colocalization intensity analysis.

0.4.0

Major update.

• the sensitivity of detection is now recalculated (i.e. calculated properly). So there could be detection differences in comparison with previous versions. The bug was caused by 0.3.7 update (so sensitivity from fixed values became a number, but was calculated as from a fixed range);
• changed the way intensity results of colocalizations are reported. Now for every particle the integrated intensity is reported in both channels. Therefore there is no need for "Detect in Ch1, quantify in Ch2".. etc option anymore, it was removed. One must notice, that detection ROIs for Ch1 are different than in Ch2 for colocalized particles. Meaning, the intensity of colocalized particle 1 from channel 1 in channel 1 could differ from intensity of colocalized particle 2 from channel 2 in channel 1. Quick estimate shows that the difference is not so big and usually one channel can be chosen as a reference channel.
• added "Preview" buttons to dialogs. In case of two channels it shows only detection, not colocalization.
• added log of plugin's parameters to the Log window.

0.3.8

• added "Segment larger particles? (slow)" option. For large particles plugin tries to split them to a subset of smaller ones based on Find maxima... function of ImageJ. It is quite costly computational procedure, so it is slow.

0.3.7

Major update. Detection is more sensitive comparing to previous versions, so results could be different.

• 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);
• area threshold in binary images is lowered, increasing overall sensitivity and making detection more robust;
• Detection's intensity threshold (sensitivity) is now a number, rather than a drop-down selection box with multiple options;
• fixed "Sort Results" function to work with Results table generated by "Measure" command (took care of hidden columns);
• Mavenization finally happened;
• fixed addition of Overlay detections in two color images in the case when there is no need for colocalization calculation;
• added an option to add detected ROIs not only to Overlay, but also to ROI Manager;

0.3.6.1

• added integrated intensity for the case of detection in one channel and quantification in another.

0.3.6

• shapes of ROIs changed from circular to rectangular;
• added possibility to include spots that are larger than the specified size;
• added integrated intensity quantification (minus BG) and ratio for a 2-channel image;
• for 2-channel image added 2 extra modes, when detection happens in only one channel and then another channel is quantified;
• fixed field names to allow scripting;

0.3.5

• image thresholding improved for non-gaussian noise (confocal-like); if the histogram is "peaked", the peak is removed;
• particle area threshold is increased giving more particles;
• fixed "Sort Results" function;

0.3.4

• image thresholding/particle detection improved;
• now gives an error message if using "Sort Results" with empty Results table;

0.3.3

• first public release;
• added variable detection levels (SNR=3,4,5,10,20,30)
• added calculation of colocalization for two-channels images;