code for generating simulated data

[zcq0730]

Would you please include the code for generating simulated data into the fissa toolbox?
Thanks a lot!

[swkeemink]

Working on this, will update here.

[zcq0730]

Thanks a lot! Looking forward.

By the way, we noticed that the roi type must be polygon.
While when the roi type is composite type, fissa runs as well. (but resulting roi region is incorrect.)
I just think might be needed to emphasize the expected roi input type, by adding a warning message.
The best would be also support for composite type roi input, if can be easily done.

[swkeemink]

The simulation code is now available in our SimCalc repository.

@zcq0730 Sorry for the delay, hopefully it is still useful! Any bugs and oddities you might run into are best asked in the SimCalc repository itself.

[zcq0730]

Thanks a lot! Definitely, it will be very useful!

[swkeemink]

@zcq0730 I also opened an issue about composite ROI types. Would it be possible to add a few more details about composite ROI types to that issue? See #68 . Thanks both for your help and interest!

[zcq0730]

Sorry for the delayed reply. Thank you very much for opening an issue on this!
In our lab, we use “brush selection tool” in ImageJ in order to precisely select ROI of individual neurons. With this tool by holding shift key we could easily draw or select an ROI that best represents the neuron(even can create a doughnut-shaped ROI, which best fit for GCaMP expression).
Details please see: https://imagej.nih.gov/ij/docs/guide/146-19.html#sub:Brush-Selection-Tool
and https://imagej.nih.gov/ij/docs/guide/146-10.html#sub:Composite-selections

Add the selected ROI which is created with this tool into ROI manager, from ROI manager click “More –> LIST” a pop-up window “Overlay Elements” will appear. One could from there find out the detailed properties of created ROI. As you would see, the created ROI type with brush selection tool is Composite type.
Details please see: https://imagej.nih.gov/ij/docs/guide/146-30.html#fig:The-ROI-Manager

Currently, FISSA could load these Composite type of ROIs and treat them as Polygon type. However, one could find out for some reason selected ROIs are recognized incorrectly. The selected ROIs are expanded to squared shape ROIs and passed to FISSA for further calculations (which would definitely compromise FISSA´s accuracy).

We have wrote an ImageJ Marco to rapidly convert all such selected Composite ROIs into Polygon ROIs (I don´t know if it could be easily done in python, I put the imageJ java code here for your convenience if you would like to implement this in python):

nROIs = roiManager("count");
for (i = 0; i < nROIs; i++)
{
roiManager("Select", i);
getSelectionCoordinates(x, y);
run("Select None");
makeSelection("polygon", x, y);
roiManager("Add");
}

Above code was inspired by the following Ref:
https://imagejdocu.tudor.lu/doku.php?id=wishlist:completed:freehand_and_selection_brush_roi_conversion
https://www.researchgate.net/post/ImageJ_How_to_count_number_of_ROIs_and_report_it_like_Analyze_particle_Summary

Thanks a lot both for your help and interest in this issue!