Inspect.md

+---
+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.
+
+* [Division events](#division-events)
+* [Find suspects on a single frame](#frame-based-suspect)
+* [Find suspects by track inspection](#track-based-suspects)
+* [Visualisation/display](#visualisation)
+
+All the current eventts are kept and saved when the segmentation is saved (by pressing <kbd>s</kbd>). They will be reloaded when an EpiCured file is loaded. The current number of events is indicated on top of the `Events` panel.
+
+To remove all events, click on `Reset suspects`.
+
+___
+
+
+# Division events
+
+Division events are detected based on the tracking graph. If cells has not been tracked yet, no division will be found.
+
+(Un)Select the option `show division` to (un)display division events. You can see the total number of divisions found written in the top of the `Inspect` panel.
+
+You can manually add a division event, or remove one.
+* To remove a division, the shortcut is the same as for removing any event: by default, press <kbd>Control+Alt+Right-click</kbd> on the event to remove.
+* To add a divison, do <kbd>Control+Shift+Left clikc</kbd> from one daughter cell to the other. EpiCure will detect automatically the most likely mother cell.
+If suspect events had been found on the two daughter cells or on the mother cell, they will be automatically removed when manually adding the division.
+
+
+
+# Frame-based suspects
+
+Cells can be suspected of being un-correctly segmented based on several static features, if their values fall out of range.
+When a cell is suspected, a point will be added in the [Suspects](#visualization) layer at the center of the cell in the frame where the suspicion has been raised.
+
+From a static frame, several features can be measured and evaluated for out of range values:
+
+* [Cell area](#cell-area)
+* [Tubeness](#tubeness)
+* [Solidity](#solidity)
+* [Intensity](#intensity)
+
+Click on the desired feature button to launch the feature inspection.
+
+### Options
+
+`only current frame`: if it is checked, only the current frame will be inspected for the given feature. Else, the inspection will be done on each frame.
+
+### Shortcuts
+
+The active layer must be the `Segmentation` layer for the shortcuts to work.
+
+### Cell area
+
+This feature measure the cell area in all frames (or only current frame if the option is checked) and test if it is above/below chosen threshold.
+Each cell (at each time point) below/above the two parameters around the `< area (pix^2) <` buttons will be flagged as suspect for area.
+
+The parameters are in pixel^2 unit. Use `0` for the min area parameter to keep all small cells, and a very high value for the max area parameter to keep all large cells.
+
+
+### Intensity
+
+This feature consider the ratio of intensity of the inner cell region compared to the cell periphery. Indeed, the peripheric part of the cell containing the junction should be much brighter while inside the cell should not be dark. If the ratio is above the chosen threshold, the cell will be marked as suspicious.
+
+### Tubeness
+
+This feature consider the ratio of linearity of the inner cell compared to the cell periphery. Indeed, the peripheric part of the cell containing the junction should be linear while inside the cell it should not be linear at all. The "linearity" is quantified by the tubeness of the intensity image. When the ratio is above the chosen threshold, the cell will be marked as suspicious.
+
+
+### Solidity
+
+Looks at the cell shape.
+Cell as detected as outliers if their solidity is greater or smaller than the vast majority of the cells **in the current frame** following Tukey's outlier scheme:
+
+```plaintext
+solidity < Q1 - k*(Q3-Q1)
+solidity > Q3 + k*(Q3-Q1)
+```
+
+`Q1` and `Q3` are the 1st and 3rd quartiles. `k` controls the range to consider a cell as outlier and can be chosen in the interface.
+
+
+---
+
+# Track-based suspects
+
+Flag suspicious segmentation based on track examination.
+
+`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.
+
+`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).
+
+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.
+
+
+
+# Visualisation
+
+:round_pushpin: **Press <kbd>x</kbd> to show/hide the suspect points.**
+
+## Suspects layer
+
+This layer contains points (shown as cross) placed at the center of each cell suspected of being not correctly segmented. Several features can be used to detect suspects, either from a static features [`Outliers options`]("outliers-options) or from analyzing the tracks [`Track options`](#track-options). 
+
+The score of the suspect is the number of suspicion (features) associated to that cell.
+
+## Display options
+
+Use the interface `Display options` in the `Suspect` onglet (right panel) to change the display of the points (the size or the color). 
+You can choose the reference feature for coloring the suspects. If a cell was suspected by the selected feature, the point will appear red, otherwise if the suspicion came from another feature, the point will appear white. The `score` feature shows the number of suspicions (features) associated to the cell from white (1) to bright red (maximum).
+
+`Go to suspect` will zoom on the selected suspect (numbered in `Suspect n°` parameter) and print in the Terminal window why this point was flag has a possible segmentation mistake. :round_pushpin: **<kbd>Ctrl+Alt+Left click</kbd> on a point to zoom on it and displays suspicion information**
+
+To directly navigate between suspects, :round_pushpin: **Press <kbd>Space</kbd> to move from one suspect to another**. The view will directly to go to the next suspect, zoom on it, and displays the information in the terminal.
+
+If the segmentation/tracking is in fact correct, you can remove the point by clicking on `Exonerate current suspect`. :round_pushpin: **<kbd>Ctrl+Alt+Right click</kbd> to remove the clicked point from suspect list**
+
+---