Inspect.md

@@ -2,6 +2,7 @@
 title: Inspect
 ---
 
+
 In EpiCure, an event is a point (a cell at a given time point) that has been detected as potentially wrongly segmented/tracked and might need manual correction (suspect) or that corresponds to a cellular event (division, extrusion..).
 
 Several features allows to detect possible segmentation/tracking errors and to display and navigate through these potential errors.
@@ -87,22 +88,41 @@ solidity > Q3 + k*(Q3-Q1)
 
 # Track-based suspects
 
-Flag suspicious segmentation based on track examination.
+__Flag suspicious segmentation based on track examination.__
+
+## Ignoring border cells
+
+Cells on the border of the tissu or imaged field are often flagged as potential errors as they can leave/enter the imaged region and thus have irregular tracks. To not flag these cells, check the `Ignore cells on` `border (of image)` and/or `tissue boundary` options.
+This will not flag any cells that touch the border of the image (for the `border` option) or that are in the periphery of the tissu (for the `boundary` option). 
+_Note that you can also know when analysing data which cells are on image border or tissue boundary in the `Output>measure cells` option if you select the `Boundary` and `Border` features._
 
-`Get potential divisions` adds points where the cell is likely divided (based on the tracking). The dividing points will be displayed as blue circle, except if the suspect display options is changed.
+## Possible errors detection
 
 `Flag track apparition` detects the sudden apparition of a new track in the movie (not on the first frame, and not on the borders of the image). If the cell is marked as a child of a division at that frame, it will not be flagged. (If two neighbor tracks are flagged in the same frame, it is likely to be an undetected division event)  
 
-`Flag track < to` flags as possibly wrong all tracks that are smaller in duration (number of frames) than the chosen parameter. For example, a cell that is present only in one frame on the whole movie is likely an error (except on the movie limits).
+`Flag track disaparition` detects the sudden disappearance of a track in the movie (not on the last frame). If the cell is marked as a parent of a division, it will not be flagged. If the cell area is below the selected threshold in the `cell area threshold` parameter, it will considered to be an extrusion and not be flagged.
+
+`Get extrusions` will add an `extrusion` event for all track that finish without being followed by a division and with the last cell area below the `cell area threshold` parameter.
+
+
+`Flag track gaps` find track that have gaps (no label in one or more frames within the track). If the option `Allow gaps` in the `advanced parameters` in the starting interface was not selected, there should not be any gaps.
+
+`Flag track smaller to` flags as possibly wrong all tracks that are smaller in duration (number of frames) than the chosen parameter. For example, a cell that is present only in one frame on the whole movie is likely an error (except on the movie limits).
+
+`Flag jump in track position`: a convenient way to notice errors in tracking or segmentation is to display the tracks (by default <kbd>r</kbd> shortcut). Errors are noticeable as sudden jump in the track (long line between two frames). This option is automatically searching for such jump in position within a track.
+The displacement between two consecutive frames of the tracking (can include a gap) is compared to the local average displacement within the track. If the difference in displacement is `jump in track position parameter` threshold above the other displacements, it will be flagged.
+Increase the value of the threshold to detect less potential jump in the track.
 
-Cells on the border of the tissu or imaged field are often flagged as potential errors as they can leave/enter the imaged region and thus have irregular tracks. To not flag these cells, check the `Ignore cells on border` option.
 
 A brutal and temporary (one or two frames only) change of value of a morphological/intensity feature of a cell within the track can reflect a segmentation error.
 The options `* variation` allow to flag such events. The associated parameter correspond to the amount of variation of the feature to flag it as suspect. Increasing it will decrease the sensitivity of the track inspection. The features that can be examined along the track are currently: size (area), shape (aspect ratio).
 
-Click on `Inspect track` to launch the analyse with the selected parameters. It will delete all previously present suspects based on track before to run. Frame-based suspects are not affected.
 
+## Inspect tracks
+
+Click on `Inspect track` to launch the analyse with the selected parameters. It will delete all previously present suspects based on track before to run. Frame-based suspects are not affected.
 
+When the process is finished, the number of `suspects` will be updated in the top of the panel and you can see each event as a point (a cross for suspect, circle for division and triangle for extrusions) in the corresponding position in the movie. 
 
 # Visualisation