elisabethkugler / zfvascularquantification Goto Github PK

Atm downsampling x,y is hard-coded 512x512 - can this be changed to user input?

Raised by @ImagingGuy:

• when no ROIset exists for segmentation > "Tell me in which folder to find ROISet" >> need to let segmentation run without need for ROI
• quantification step requires ROI >> need to let quantification run without need for ROI

Issue raised by @ImagingGuy

• can we examine multiscale TF in more depth? i.e. when vessel diameters span a large range, can multiscale be integrated
  (note EK: Frangi filter does not really work on the data we studied https://etheses.whiterose.ac.uk/27497/;
  that's why we went for Sato -- however it seems that the current TF/Sato implementation is not truly multiscale)

Had a user attempt to run the ZFVascQuant_GUI_02122020.ijm macro file pointing at a directory path that contained spaces.

This can be overcome by modifying Line155 of that code to include [square brackets] around the path +filename
eg. run("Bio-Formats Importer", "open=[" + path + filelist[i] + "] autoscale color_mode=Default split_channels view=Hyperstack stack_order=XYCZT");

Line 197 creates a directory which contains a link to the github repository. This link is not compatible for windows as the file path slashes point the wrong way.

The command File.separator; can be used to match the system file seperator if required (eg. fs = File.separator; ) but would likely result in excess subdirectories anyway.

Perhaps making a .txt file in the directory with the relevant github directory could be of use, or printing this info into the log window.