diff --git a/1_identify_fibers.py b/1_identify_fibers.py
index 74d312bd229c0e36e582708df3471be31124944d..66afc8e834c10092abf57b1840e803255c02b83c 100755
--- a/1_identify_fibers.py
+++ b/1_identify_fibers.py
@@ -12,7 +12,6 @@
# @ Integer (label="Min perimeter [um]", value=5) minPer
# @ Integer (label="Max perimeter [um]", value=300) maxPer
# @ String (visibility=MESSAGE, value="<html><b> Expand ROIS to match fibers </b></html>") msg3
-# @ Double (label="ROI expansion [microns]", value=1) enlarge_radius
# @ String (visibility=MESSAGE, value="<html><b> channel positions in the hyperstack </b></html>") msg5
# @ Integer (label="Membrane staining channel number", style="slider", min=1, max=5, value=1) membrane_channel
# @ Integer (label="Fiber staining (MHC) channel number (0=skip)", style="slider", min=0, max=5, value=3) fiber_channel
@@ -63,7 +62,7 @@ from fiji.plugin.trackmate.tracking.jaqaman import SparseLAPTrackerFactory
from ij import IJ
from ij import WindowManager as wm
from ij.measure import ResultsTable
-from ij.plugin import Duplicator, ImageCalculator, RoiEnlarger
+from ij.plugin import Duplicator, ImageCalculator
from imcflibs import pathtools
from imcflibs.imagej import bioformats as bf
from imcflibs.imagej import misc
@@ -490,26 +489,6 @@ def save_selected_rois(rm, selected_rois, target):
rm.runCommand("Deselect")
-def enlarge_all_rois(amount_in_um, rm, pixel_size_in_um):
- """Enlarges all ROIs in the RoiManager by x scaled units.
-
- Parameters
- ----------
- amount_in_um : float
- the value by which to enlarge in scaled units, e.g 3.5
- rm : RoiManager
- a reference of the IJ-RoiManager
- pixel_size_in_um : float
- the pixel size, e.g. 0.65 px/um
- """
- amount_px = amount_in_um / pixel_size_in_um
- all_rois = rm.getRoisAsArray()
- rm.reset()
- for roi in all_rois:
- enlarged_roi = RoiEnlarger.enlarge(roi, amount_px)
- rm.addRoi(enlarged_roi)
-
-
def select_positive_fibers(imp, channel, rm, min_intensity):
"""Select ROIs in ROIManager based on intensity in specific channel.
@@ -735,7 +714,6 @@ if __name__ == "__main__":
IJ.log("area = " + str(minAr) + "-" + str(maxAr))
IJ.log("perimeter = " + str(minPer) + "-" + str(maxPer))
IJ.log("circularity = " + str(minCir) + "-" + str(maxCir))
- IJ.log("ROI expansion [microns] = " + str(enlarge_radius))
IJ.log("Membrane channel = " + str(membrane_channel))
IJ.log("MHC positive fiber channel = " + str(fiber_channel))
# IJ.log("sub-tiling = " + str(tiling_factor))
@@ -793,8 +771,6 @@ if __name__ == "__main__":
misc.timed_log("Getting the ROIs")
command.run(Labels2Rois, True, "rm", rm, "imp", imp_result).get()
- misc.timed_log("Enlarging and renumbering the ROIs")
- enlarge_all_rois(enlarge_radius, rm, raw_image_calibration.pixelWidth)
renumber_rois(rm)
misc.timed_log("Saving the ROIs")