Update the trackmate-mask-detector page and add a 2nd tutorial.

By Joanna.
imagej · Jul 26, 2021 · 23f7392 · 23f7392
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diff --git a/_pages/plugins/trackmate/trackmate-mask-detector.md b/_pages/plugins/trackmate/trackmate-mask-detector.md
@@ -31,7 +31,7 @@ This movie is a maximum-intensity projection (MIP) of a longer movie used initia
 
 This is very short movie, that stops after the 2nd cell division. We made a MIP so that this movie can be used in this tutorial.
 
-## The image.
+### The image.
 
 Open the image `CelegansEarly_MIP.tif` in Fiji. 
 
@@ -43,31 +43,31 @@ The 2nd channel contains the segmentation results of this signal, that I obtaine
 - Gaussian blur filter;
 - Plain thresholding.
 
-{% include img src='/media/plugins/trackmate/trackmate-mask-tutorial-1.png' %}
+{% include img src='/media/plugins/trackmate/trackmate-mask-tutorial-1.png' align='center' %}
 
-## Running TrackMate.
+### Running TrackMate.
 
 Launch TrackMate: {% include bc path='Plugins>Tracking>TrackMate' %}
 
 In the second panel, select the `Mask detector`
 
-{% include img src='/media/plugins/trackmate/trackmate-mask-tutorial-2.png' width='250' %}
+{% include img src='/media/plugins/trackmate/trackmate-mask-tutorial-2.png' width='250' align='center'%}
 
 The configuration panel is very simple:
 
-{% include img src='/media/plugins/trackmate/trackmate-mask-tutorial-3.png' width='350' %}
+{% include img src='/media/plugins/trackmate/trackmate-mask-tutorial-3.png' width='350' align='center'%}
 
 You just need to specify in what channel is the mask. In our case it is the second one. 
 
 There is a checkbox that lets you simplify contours. We suggest you leave it on by default. The details of contour simplification are explained [here](/plugins/trackmate/trackmate-v7-detectors#simplifying-contours). 
 
 The `Preview` button will show the results. In frame 11 for instance, 6 objects are detected with their contour:
 
-{% include img src='/media/plugins/trackmate/trackmate-mask-tutorial-4.png' width='350' %}
+{% include img src='/media/plugins/trackmate/trackmate-mask-tutorial-4.png' width='350' align='center'%}
 
 The click the `Next` button. In total 78 spots are found in this movie. You can track them with `LAP tracker`, enabling the detection of split events so that we can deal with the 2 cell divisions. In the end of tracking process we get this:
 
-{% include img src='/media/plugins/trackmate/trackmate-mask-tutorial-5.png'  %}
+{% include img src='/media/plugins/trackmate/trackmate-mask-tutorial-5.png'  align='center'%}
 
 Notice that we have false divisions due to the motile polar body, that gets wrongly attached to the top cell movie. We could correct this either manually, or by filtering out the polar bodies based on their `Area`. We leave this correction as an exercise to the reader.
 
@@ -77,15 +77,15 @@ Now that we have the cell shape and their lineage, we can follow how the shape c
 
 To do this, select the bottom cell by clicking in one of the spot, then moved to the `Plot feature` panel of the TrackMate wizard. Make sure you are in the `Spots` tab.
 
-{% include img src='/media/plugins/trackmate/trackmate-mask-tutorial-6.png'  %}
+{% include img src='/media/plugins/trackmate/trackmate-mask-tutorial-6.png'  align='center'%}
 
 In this panel, select the `Area` in the `Feature for Y axis` first list.
 
 Click on the green `+` button to add a second list of features, and select the `Circularity` feature. We want to plot these feature values not for a single spot, nor for the whole dataset, but just for the track of the spot we selected. To do this, select the `Tracks of selection` radio button at the bottom. Of course, at least one spot in the track of interest must be selected.
 
 Click on the `Plot features` button. The two graphs appear:
 
-{% include img src='/media/plugins/trackmate/trackmate-mask-tutorial-7.png'  width='400' %}
+{% include img src='/media/plugins/trackmate/trackmate-mask-tutorial-7.png'  width='400' align='center'%}
 
 (You might have to deselect the cell by clicking elsewhere, then clicking back in the graph so that it shows the same color than above.)
 
@@ -95,39 +95,87 @@ The circularity is plotted on the second graph. It remains high almost all the t
 
 As a side note, if you right-click on any of the 2 plots, you will have this popup menu that will let you export the graph as a pdf, png or svg image, or show its data in a table that can saved to a CSV file.
 
-{% include img src='/media/plugins/trackmate/trackmate-mask-tutorial-8.png' width='400'  %}
+{% include img src='/media/plugins/trackmate/trackmate-mask-tutorial-8.png' width='400'  align='center'%}
 
 ### Editing the mask.
 
 If we repeat the above procedure for the top cell, we have the following graphs:
 
-{% include img src='/media/plugins/trackmate/trackmate-mask-tutorial-9.png' width='400'  %}
+{% include img src='/media/plugins/trackmate/trackmate-mask-tutorial-9.png' width='400' align='center' %}
 
 Note that at t=16 minutes, one of the daughter nuclei has a circularity that shows a sharp drop. By inspecting the image, we can see that this is caused by the object contour to be incorrect for this spot. The motile polar body went too close to the nucleus and the mask merged them together. So we end up in having an artificially elongated object, which results in a low circularity.
 
 Right now there is no way to edit a spot contour. Here we would suggest a hack. We will directly edit the binary mask by cutting the object with Fiji tool.
 
 Go back to the first panel of the TrackMate wizard and in the image display, select the 9th time-point, and make the second channel active:
 
-{% include img src='/media/plugins/trackmate/trackmate-mask-tutorial-10.png' width='250'  %}
+{% include img src='/media/plugins/trackmate/trackmate-mask-tutorial-10.png' width='250'  align='center'%}
 
 Let's zoom on the nucleus with the defective mask.
 
-{% include img src='/media/plugins/trackmate/trackmate-mask-tutorial-11.png' width='250'  %}
+{% include img src='/media/plugins/trackmate/trackmate-mask-tutorial-11.png' width='250'  align='center'%}
 
 We will make a cut in the mask to separate the nucleus from the polar body. We can use the Image ROI to do so. In the ImageJ toolbar, select the line ROI tool. Double click on the color selection tool, and select the black color as the foreground color. Now draw a line that goes between the nucleus and the polar body.
 
-{% include img src='/media/plugins/trackmate/trackmate-mask-tutorial-12.png' width='250'  %}
+{% include img src='/media/plugins/trackmate/trackmate-mask-tutorial-12.png' width='250'  align='center'%}
 
 Press the `D` key to draw. Since we picked the black color, the pixels along the line ROI will be replaced by a pixel value of 0, cutting the mask into 2 components:
 
-{% include img src='/media/plugins/trackmate/trackmate-mask-tutorial-13.png' width='400'  %}
+{% include img src='/media/plugins/trackmate/trackmate-mask-tutorial-13.png' width='400'  align='center'%}
 
 Now you can proceed with the tracking as before. The polar body and the nucleus will be segmented as two spots:
 
-{% include img src='/media/plugins/trackmate/trackmate-mask-tutorial-14.png' width='400'  %}
+{% include img src='/media/plugins/trackmate/trackmate-mask-tutorial-14.png' width='400'  align='center'%}
 
 Right now, this is the only way to edit the spot contour in TrackMate. Which means it is important to get a good segmentation _results_ before running TrackMate.
 
 {% include person id='tinevez' %}  July 2021
 
+## Tutorial: Cancer cells migration.
+
+TODO! Link to demo image.
+
+- Open Fiji.
+- Open your image.
+- Open TrackMate {% include bc path='Plugins | Tracking | TrackMate' %}. The start panel will launch, showing information about the image dimensions. Click `Next`.
+- The “Select a detector” -panel opens. From the pull-down menu, select the `Mask detector`. Click `Next`.
+
+{% include img src='/media/plugins/trackmate/trackmate-mask-detector-tutorial-bis-1.png' align='center' width='250'  %}
+
+- A panel with the description of the mask detector opens. Here you can select to Simplify the contours to smooth the edges of the segmented objects. Click on `Preview` to see a preview of the segmentation. On the left, there will also be the number of detected objects in that field of view. Click `Next`. The objects are now being detected.
+- When the progress bar has reached the end, click `Next`.
+- A panel to filter the detected spots according to their quality opens (more information about this filtering can be found[ ](https://www.google.com/url?q=https://imagej.net/plugins/trackmate/getting-started%23initial-spot-filtering&sa=D&source=editors&ust=1627290029831000&usg=AOvVaw07FRzNH1si7etp26p4FTqx)[here](/plugins/trackmate/getting-started#initial-spot-filtering). With our test image, this part can be ignored. Click `Next`.
+- A panel to filter spots according to their properties (i.e. size, shape, location, or signal intensity) opens.  With our test image, we do not need to filter any spots. Click `Next`.
+
+{% include img src='/media/plugins/trackmate/trackmate-mask-detector-tutorial-bis-2.png' align='center' width='250'  %}
+
+- A tracking panel opens. In this panel, you can select a method for tracking your objects. In this exercise, we use the `LAP tracker`. Please select it from the pull-down menu, and click `Next`.
+- A panel to choose the LAP tracker settings opens. First, with the `Frame to Frame linking` parameter, you give the maximum distance to link two objects between frames. With our test image, we use **20 microns**. Tick the `Allow gap closing` box and add values: `Max distance`: **20 microns** and `Max frame gap`: **5**. Next, you let TrackMate know if the tracks are allowed to split. Track splitting can occur, for example, due to cell division. Tick the box `Allow track segment splitting` and insert value `Max distance`: **20 microns**. Below you will also see a setting to allow Track segment merging. This box should remain unticked as we do not expect the nuclei to merge here. Click `Next`.
+
+{% include img src='/media/plugins/trackmate/trackmate-mask-detector-tutorial-bis-3.png' align='center' width='250'  %}
+
+- A Track filter panel opens. In this panel, you can remove tracks according to their properties (*i.e.*, length, speed, or location). With our test image, we do not need to filter any tracks. Click `Next`.
+
+- A window with track visualization options opens. Here it is possible to edit track or object colours according to their properties. We will label the tracked objects according to their mean speed and the tracks according to the total distance travelled.
+  - First, make sure that the `Display spots` and `as ROIs` boxes are ticked.
+  -  Select `Track mean speed` from the Color spots by clicking on the pull-down menu and then click `auto`.
+  - To fill the objects with the indicative colour, click on `Edit settings`. This will open a new panel with display settings. Here, tick the box `draw spots filled`.
+  - From the same panel, also set the `line thickness` as **2**.
+  - Close the Display settings window.
+  - Make sure the `Display tracks` box is ticked.
+  - From the pulldown menu, select `Show tracks forward in time`. This will show the future trajectories of the object movements.
+  - From the Color tracks pull-down menu, select `Total distance travelled`. And click `auto`.
+
+- In this panel, you can also export the results as .csv files. Please do so by clicking on **Tracks** at the bottom of the panel. A window with a lot of data will open. Ensure you export the **Spots** (information about the spot) and the **Tracks** (information about the tracks) files. Close the results window and click **Next**.
+
+{% include img src='/media/plugins/trackmate/trackmate-mask-detector-tutorial-bis-4.png' align='center' width='600'  %}
+
+- In this panel, you have access to many plotting features- again, click `Next`.
+- Here you have the possibility to do different actions. For this exercise, we will export a tracking image of our experiment. Then from the pull-down menu, select `Capture overlay`. After clicking on `Execute`, a pop-up window opens. Here you can define the time interval you want to save and click `OK`. TrackMate will generate a video of your experiment. Remember to save the image from {% include bc path='File | Save as...' %}.
+
+You can see on the resulting movie that some touching cells were incorrectly identified as one object. This is a problem with mask images. You can fix this by editing the mask as we did in the first tutorial above, or moving back to the raw image and use the [StarDist detector](/plugins/trackmate/trackmate-stardist) we introduce elsewhere.
+
+{% include img src='/media/plugins/trackmate/trackmate-mask-detector-tutorial-bis-5.gif' align='center'  %}
+
+Joanna W. Pylvänäinen - July 2021
+
diff --git a/media/plugins/trackmate/trackmate-mask-detector-tutorial-bis-1.png b/media/plugins/trackmate/trackmate-mask-detector-tutorial-bis-1.png
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diff --git a/media/plugins/trackmate/trackmate-mask-detector-tutorial-bis-3.png b/media/plugins/trackmate/trackmate-mask-detector-tutorial-bis-3.png
diff --git a/media/plugins/trackmate/trackmate-mask-detector-tutorial-bis-4.png b/media/plugins/trackmate/trackmate-mask-detector-tutorial-bis-4.png
diff --git a/media/plugins/trackmate/trackmate-mask-detector-tutorial-bis-5.gif b/media/plugins/trackmate/trackmate-mask-detector-tutorial-bis-5.gif