diff --git a/2d_spots_in_fibers.py b/2d_spots_in_fibers.py
index 3924854022bf9f6da243ce5317da666ac062797f..22b3a45e44b30e642e4050db67a9cdbffeadd179 100644
--- a/2d_spots_in_fibers.py
+++ b/2d_spots_in_fibers.py
@@ -30,7 +30,7 @@ from loci.formats import ImageReader, MetadataTools, Memoizer
 # MorpholibJ imports
 from inra.ijpb.binary import BinaryImages
 # BIOP imports
-from ch.epfl.biop.ij2command import Labels2Rois, Rois2Labels
+from ch.epfl.biop.ij2command import Labels2Rois
 # python imports
 import os
 
@@ -330,7 +330,7 @@ def measure_intensity_sum(imp, rm):
 
     Example
     -------
-    >>> labels, intensities = measure_intensity_sum(image, roi_manager)
+    >>> labels, intensities = measure_intensity_sum(imp, roi_manager)
     """
 
     rt_ = ResultsTable()
@@ -428,17 +428,6 @@ def load_rois_from_zip(path):
     rm.runCommand("Open", path)
 
 
-def convert_rois_to_labelimage(imp):
-    rm = RoiManager.getInstance()
-    if not rm:
-        rm = RoiManager()
-
-    label_imp = command.run( Rois2Labels , False , 'imp' , imp , 'rm', rm).get().getOutput("label_imp")
-    rm.reset() # TODO: should be optional but can be default
-
-    return label_imp
-
-
 def close_images(list_of_imps):
     """Close given ImagePlus images
 
@@ -468,11 +457,6 @@ if threshold <= 0:
     threshold = get_threshold_from_method(dapi_channel, "otsu")
 dapi_binary = convert_to_binary(dapi_channel, threshold)
 
-# Get the fiber segmentation from ij roizip and convert to labelimage
-load_rois_from_zip(fiber_segmentation_roiset)
-fibers_label_imp = convert_rois_to_labelimage(dapi_channel)
-dapi_channel.close()
-
 # detect spots and count them per fiber
 results_table = ResultsTable()
 for index, channel in enumerate(processing_channels):
@@ -480,7 +464,7 @@ for index, channel in enumerate(processing_channels):
     quality_threshold = float(quality_thresholds[index])
     spots_channel = BFopen_image(path_to_image, channel, series_number)
     spots_label_imp = run_trackmate_dog_spot_detector(spots_channel, spot_diameter, quality_threshold)
-    save_image_as_IJtif(spots_label_imp, filename, "spots_ch" + str(channel), parent_dir)
+    # save_image_as_IJtif(spots_label_imp, filename, "spots_ch" + str(channel), parent_dir)
     save_labelimage_as_ijroiset(spots_label_imp, filename, "spots_ch" + str(channel), parent_dir)
     spots_binary_imp = convert_labelimage_to_binary(spots_label_imp)
     dapi_positive_spots_binary = ImageCalculator.run(spots_binary_imp, dapi_binary, "Multiply create")