diff --git a/analysis_results/Munc13DKO/CTRL/AZ_distances_with_seg_id.csv b/analysis_results/Munc13DKO/CTRL/AZ_distances_with_seg_id.csv
new file mode 100644
index 0000000..30a4c53
--- /dev/null
+++ b/analysis_results/Munc13DKO/CTRL/AZ_distances_with_seg_id.csv
@@ -0,0 +1,132 @@
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diff --git a/analysis_results/Munc13DKO/CTRL/AZ_distances_within_100_with_seg_id.csv b/analysis_results/Munc13DKO/CTRL/AZ_distances_within_100_with_seg_id.csv
new file mode 100644
index 0000000..c7ff721
--- /dev/null
+++ b/analysis_results/Munc13DKO/CTRL/AZ_distances_within_100_with_seg_id.csv
@@ -0,0 +1,44 @@
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diff --git a/analysis_results/Munc13DKO/CTRL/AZ_distances_within_200_with_seg_id.csv b/analysis_results/Munc13DKO/CTRL/AZ_distances_within_200_with_seg_id.csv
new file mode 100644
index 0000000..b89f277
--- /dev/null
+++ b/analysis_results/Munc13DKO/CTRL/AZ_distances_within_200_with_seg_id.csv
@@ -0,0 +1,74 @@
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diff --git a/analysis_results/Munc13DKO/CTRL/AZ_distances_within_40_with_diameters_and_seg_id.csv b/analysis_results/Munc13DKO/CTRL/AZ_distances_within_40_with_diameters_and_seg_id.csv
new file mode 100644
index 0000000..b69d222
--- /dev/null
+++ b/analysis_results/Munc13DKO/CTRL/AZ_distances_within_40_with_diameters_and_seg_id.csv
@@ -0,0 +1,18 @@
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diff --git a/analysis_results/Munc13DKO/CTRL/AZ_distances_within_40_with_seg_id.csv b/analysis_results/Munc13DKO/CTRL/AZ_distances_within_40_with_seg_id.csv
new file mode 100644
index 0000000..4d5b09c
--- /dev/null
+++ b/analysis_results/Munc13DKO/CTRL/AZ_distances_within_40_with_seg_id.csv
@@ -0,0 +1,18 @@
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diff --git a/analysis_results/Munc13DKO/KO/AZ_distances_with_seg_id.csv b/analysis_results/Munc13DKO/KO/AZ_distances_with_seg_id.csv
new file mode 100644
index 0000000..86120e7
--- /dev/null
+++ b/analysis_results/Munc13DKO/KO/AZ_distances_with_seg_id.csv
@@ -0,0 +1,80 @@
+,A_M13DKO_080212_DKO1.2_crop_seg_id,A_M13DKO_080212_DKO1.2_crop_distance,G_M13DKO_060212_DKO1.1_crop_seg_id,G_M13DKO_060212_DKO1.1_crop_distance,C_M13DKO_080212_DKO1.2_crop_seg_id,C_M13DKO_080212_DKO1.2_crop_distance,E_M13DKO_080212_DKO1.2_crop_seg_id,E_M13DKO_080212_DKO1.2_crop_distance,H_M13DKO_080212_DKO1.2_crop_seg_id,H_M13DKO_080212_DKO1.2_crop_distance
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diff --git a/analysis_results/Munc13DKO/KO/AZ_distances_within_100_with_seg_id.csv b/analysis_results/Munc13DKO/KO/AZ_distances_within_100_with_seg_id.csv
new file mode 100644
index 0000000..080305c
--- /dev/null
+++ b/analysis_results/Munc13DKO/KO/AZ_distances_within_100_with_seg_id.csv
@@ -0,0 +1,21 @@
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diff --git a/analysis_results/Munc13DKO/KO/AZ_distances_within_200_with_seg_id.csv b/analysis_results/Munc13DKO/KO/AZ_distances_within_200_with_seg_id.csv
new file mode 100644
index 0000000..3275c5a
--- /dev/null
+++ b/analysis_results/Munc13DKO/KO/AZ_distances_within_200_with_seg_id.csv
@@ -0,0 +1,42 @@
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diff --git a/analysis_results/Munc13DKO/KO/AZ_distances_within_40_with_diameters_and_seg_id.csv b/analysis_results/Munc13DKO/KO/AZ_distances_within_40_with_diameters_and_seg_id.csv
new file mode 100644
index 0000000..eebe360
--- /dev/null
+++ b/analysis_results/Munc13DKO/KO/AZ_distances_within_40_with_diameters_and_seg_id.csv
@@ -0,0 +1,9 @@
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diff --git a/analysis_results/Munc13DKO/KO/AZ_distances_within_40_with_seg_id.csv b/analysis_results/Munc13DKO/KO/AZ_distances_within_40_with_seg_id.csv
new file mode 100644
index 0000000..9bfed95
--- /dev/null
+++ b/analysis_results/Munc13DKO/KO/AZ_distances_within_40_with_seg_id.csv
@@ -0,0 +1,9 @@
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diff --git a/analysis_results/SNAP25/CTRL/with_segID/AZ_distances_with_seg_id.csv b/analysis_results/SNAP25/CTRL/with_segID/AZ_distances_with_seg_id.csv
new file mode 100644
index 0000000..33ee2f8
--- /dev/null
+++ b/analysis_results/SNAP25/CTRL/with_segID/AZ_distances_with_seg_id.csv
@@ -0,0 +1,94 @@
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diff --git a/analysis_results/SNAP25/CTRL/with_segID/AZ_distances_within_100_with_seg_id.csv b/analysis_results/SNAP25/CTRL/with_segID/AZ_distances_within_100_with_seg_id.csv
new file mode 100644
index 0000000..d726d08
--- /dev/null
+++ b/analysis_results/SNAP25/CTRL/with_segID/AZ_distances_within_100_with_seg_id.csv
@@ -0,0 +1,23 @@
+,E_SNAP25_120812_CTRL2.3_14_crop_seg_id,E_SNAP25_120812_CTRL2.3_14_crop_distance,C_SNAP25_12082_CTRL2.3_5_crop_seg_id,C_SNAP25_12082_CTRL2.3_5_crop_distance,D_SNAP25_12082_CTRL2.3_5_crop_seg_id,D_SNAP25_12082_CTRL2.3_5_crop_distance,B_SNAP25_120812_CTRL1.4_4_crop_seg_id,B_SNAP25_120812_CTRL1.4_4_crop_distance,B_SNAP25_120812_CTRL1.3_13_crop_seg_id,B_SNAP25_120812_CTRL1.3_13_crop_distance
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diff --git a/analysis_results/SNAP25/CTRL/with_segID/AZ_distances_within_200_with_seg_id.csv b/analysis_results/SNAP25/CTRL/with_segID/AZ_distances_within_200_with_seg_id.csv
new file mode 100644
index 0000000..ff92602
--- /dev/null
+++ b/analysis_results/SNAP25/CTRL/with_segID/AZ_distances_within_200_with_seg_id.csv
@@ -0,0 +1,57 @@
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diff --git a/analysis_results/SNAP25/CTRL/with_segID/AZ_distances_within_40_with_diameters_and_seg_id.csv b/analysis_results/SNAP25/CTRL/with_segID/AZ_distances_within_40_with_diameters_and_seg_id.csv
new file mode 100644
index 0000000..e3f77b1
--- /dev/null
+++ b/analysis_results/SNAP25/CTRL/with_segID/AZ_distances_within_40_with_diameters_and_seg_id.csv
@@ -0,0 +1,11 @@
+,E_SNAP25_120812_CTRL2.3_14_crop_seg_id,E_SNAP25_120812_CTRL2.3_14_crop_distance,E_SNAP25_120812_CTRL2.3_14_crop_diameter,C_SNAP25_12082_CTRL2.3_5_crop_seg_id,C_SNAP25_12082_CTRL2.3_5_crop_distance,C_SNAP25_12082_CTRL2.3_5_crop_diameter,D_SNAP25_12082_CTRL2.3_5_crop_seg_id,D_SNAP25_12082_CTRL2.3_5_crop_distance,D_SNAP25_12082_CTRL2.3_5_crop_diameter,B_SNAP25_120812_CTRL1.4_4_crop_seg_id,B_SNAP25_120812_CTRL1.4_4_crop_distance,B_SNAP25_120812_CTRL1.4_4_crop_diameter,B_SNAP25_120812_CTRL1.3_13_crop_seg_id,B_SNAP25_120812_CTRL1.3_13_crop_distance,B_SNAP25_120812_CTRL1.3_13_crop_diameter
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diff --git a/analysis_results/SNAP25/CTRL/with_segID/AZ_distances_within_40_with_seg_id.csv b/analysis_results/SNAP25/CTRL/with_segID/AZ_distances_within_40_with_seg_id.csv
new file mode 100644
index 0000000..238eaa5
--- /dev/null
+++ b/analysis_results/SNAP25/CTRL/with_segID/AZ_distances_within_40_with_seg_id.csv
@@ -0,0 +1,11 @@
+,E_SNAP25_120812_CTRL2.3_14_crop_seg_id,E_SNAP25_120812_CTRL2.3_14_crop_distance,C_SNAP25_12082_CTRL2.3_5_crop_seg_id,C_SNAP25_12082_CTRL2.3_5_crop_distance,D_SNAP25_12082_CTRL2.3_5_crop_seg_id,D_SNAP25_12082_CTRL2.3_5_crop_distance,B_SNAP25_120812_CTRL1.4_4_crop_seg_id,B_SNAP25_120812_CTRL1.4_4_crop_distance,B_SNAP25_120812_CTRL1.3_13_crop_seg_id,B_SNAP25_120812_CTRL1.3_13_crop_distance
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+9,,,,,,,89,39.558381766700215,,
diff --git a/analysis_results/SNAP25/KO/with_segID/AZ_distances_with_seg_id.csv b/analysis_results/SNAP25/KO/with_segID/AZ_distances_with_seg_id.csv
new file mode 100644
index 0000000..d4cc740
--- /dev/null
+++ b/analysis_results/SNAP25/KO/with_segID/AZ_distances_with_seg_id.csv
@@ -0,0 +1,43 @@
+,D_SNAP25_12.08.12_KO1.1_3_crop_seg_id,D_SNAP25_12.08.12_KO1.1_3_crop_distance,C_SNAP25_12082_KO1.2_6_crop_seg_id,C_SNAP25_12082_KO1.2_6_crop_distance,E_SNAP25_12082_KO2.1_6_crop_seg_id,E_SNAP25_12082_KO2.1_6_crop_distance,A_SNAP25_12082_KO1.2_6_crop_seg_id,A_SNAP25_12082_KO1.2_6_crop_distance,B_SNAP25_12082_KO1.2_6_crop_seg_id,B_SNAP25_12082_KO1.2_6_crop_distance
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+14,2.0,116.82938513918492,,,5.0,214.6602249975528,6,136.35409155577256,25.0,161.81013340331936
+15,4.0,117.55062463466538,,,,,41,165.7251932205843,13.0,169.13632057012472
+16,14.0,149.57199545369448,,,,,39,167.86077531097013,37.0,174.35990801786974
+17,12.0,170.03345068544604,,,,,3,197.68199389929276,26.0,192.21918426629537
+18,11.0,170.26763221469898,,,,,30,199.64515666551995,38.0,193.06534764167287
+19,5.0,180.93926111267285,,,,,42,210.15803273727133,36.0,193.95762797064725
+20,,,,,,,32,215.83823701096156,20.0,198.12128776080576
+21,,,,,,,7,217.7541633585912,12.0,205.73927103982848
+22,,,,,,,31,223.82455723177475,7.0,219.64788150127922
+23,,,,,,,20,240.9652263377436,32.0,226.74558791738374
+24,,,,,,,5,247.78869889484469,24.0,227.2456022544771
+25,,,,,,,26,250.931304910328,8.0,244.34889642476392
+26,,,,,,,22,252.1936610860789,18.0,250.5797895202245
+27,,,,,,,4,258.6044639753924,35.0,254.04929642886242
+28,,,,,,,40,266.5098673445319,22.0,267.56793480535
+29,,,,,,,24,268.03684634766165,39.0,271.812325151013
+30,,,,,,,19,280.03925114883447,14.0,287.284126286156
+31,,,,,,,34,289.24027207150806,30.0,305.54580285777126
+32,,,,,,,37,299.587663390868,21.0,314.7108989342441
+33,,,,,,,36,300.9669155305945,19.0,316.49757610446244
+34,,,,,,,35,314.46909259893886,10.0,320.2710681594577
+35,,,,,,,25,318.0009551872447,34.0,338.03697325588513
+36,,,,,,,23,320.66292015760104,23.0,345.3028563218092
+37,,,,,,,21,331.09683148589625,9.0,360.6920704257303
+38,,,,,,,29,334.8933096853384,17.0,375.15825913339563
+39,,,,,,,38,343.8907550894615,,
+40,,,,,,,33,363.57622585642207,,
+41,,,,,,,28,388.3818780427326,,
diff --git a/analysis_results/SNAP25/KO/with_segID/AZ_distances_within_100_with_seg_id.csv b/analysis_results/SNAP25/KO/with_segID/AZ_distances_within_100_with_seg_id.csv
new file mode 100644
index 0000000..f0d0a65
--- /dev/null
+++ b/analysis_results/SNAP25/KO/with_segID/AZ_distances_within_100_with_seg_id.csv
@@ -0,0 +1,14 @@
+,D_SNAP25_12.08.12_KO1.1_3_crop_seg_id,D_SNAP25_12.08.12_KO1.1_3_crop_distance,C_SNAP25_12082_KO1.2_6_crop_seg_id,C_SNAP25_12082_KO1.2_6_crop_distance,E_SNAP25_12082_KO2.1_6_crop_seg_id,E_SNAP25_12082_KO2.1_6_crop_distance,A_SNAP25_12082_KO1.2_6_crop_seg_id,A_SNAP25_12082_KO1.2_6_crop_distance,B_SNAP25_12082_KO1.2_6_crop_seg_id,B_SNAP25_12082_KO1.2_6_crop_distance
+0,9.0,9.193587982936805,4.0,1.554,8.0,3.4748496370346733,13,4.662,1.0,6.216
+1,10.0,10.878,9.0,1.554,6.0,5.154034924212291,1,7.77,27.0,10.308069848424582
+2,13.0,12.90849348297469,7.0,4.662,11.0,6.216,9,9.452612972083434,3.0,40.582911576179455
+3,15.0,14.660406679215962,8.0,6.216,12.0,6.407306142209845,11,11.419521180855176,6.0,60.04556260041203
+4,18.0,22.46591738612069,5.0,13.636294658007358,14.0,6.407306142209845,17,41.14433273246754,29.0,75.15642703056074
+5,17.0,59.642026021925176,1.0,60.76517558602131,13.0,77.0602260832396,16,50.13908212163442,28.0,89.87710509356651
+6,7.0,63.581203071348064,3.0,86.46721885200193,7.0,80.34345317448087,14,51.11691610416262,2.0,90.78605789437054
+7,16.0,76.22524447976537,,,10.0,90.4796399197079,15,56.35259124476886,5.0,92.88969193618848
+8,1.0,97.60555117410075,,,1.0,90.51966630517371,2,65.1012870840508,,
+9,,,,,,,10,76.60447689267252,,
+10,,,,,,,12,91.686,,
+11,,,,,,,8,96.67328958921384,,
+12,,,,,,,27,99.94044514609688,,
diff --git a/analysis_results/SNAP25/KO/with_segID/AZ_distances_within_200_with_seg_id.csv b/analysis_results/SNAP25/KO/with_segID/AZ_distances_within_200_with_seg_id.csv
new file mode 100644
index 0000000..fd5f931
--- /dev/null
+++ b/analysis_results/SNAP25/KO/with_segID/AZ_distances_within_200_with_seg_id.csv
@@ -0,0 +1,22 @@
+,D_SNAP25_12.08.12_KO1.1_3_crop_seg_id,D_SNAP25_12.08.12_KO1.1_3_crop_distance,C_SNAP25_12082_KO1.2_6_crop_seg_id,C_SNAP25_12082_KO1.2_6_crop_distance,E_SNAP25_12082_KO2.1_6_crop_seg_id,E_SNAP25_12082_KO2.1_6_crop_distance,A_SNAP25_12082_KO1.2_6_crop_seg_id,A_SNAP25_12082_KO1.2_6_crop_distance,B_SNAP25_12082_KO1.2_6_crop_seg_id,B_SNAP25_12082_KO1.2_6_crop_distance
+0,9.0,9.193587982936805,4.0,1.554,8.0,3.4748496370346733,13.0,4.662,1,6.216
+1,10.0,10.878,9.0,1.554,6.0,5.154034924212291,1.0,7.77,27,10.308069848424582
+2,13.0,12.90849348297469,7.0,4.662,11.0,6.216,9.0,9.452612972083434,3,40.582911576179455
+3,15.0,14.660406679215962,8.0,6.216,12.0,6.407306142209845,11.0,11.419521180855176,6,60.04556260041203
+4,18.0,22.46591738612069,5.0,13.636294658007358,14.0,6.407306142209845,17.0,41.14433273246754,29,75.15642703056074
+5,17.0,59.642026021925176,1.0,60.76517558602131,13.0,77.0602260832396,16.0,50.13908212163442,28,89.87710509356651
+6,7.0,63.581203071348064,3.0,86.46721885200193,7.0,80.34345317448087,14.0,51.11691610416262,2,90.78605789437054
+7,16.0,76.22524447976537,12.0,118.81750265007256,10.0,90.4796399197079,15.0,56.35259124476886,5,92.88969193618848
+8,1.0,97.60555117410075,11.0,144.34644175732217,1.0,90.51966630517371,2.0,65.1012870840508,4,103.85092612008812
+9,3.0,102.0801770178716,2.0,198.70550218854032,15.0,113.29288830284098,10.0,76.60447689267252,16,123.66755042451517
+10,6.0,104.9726712435194,,,2.0,133.30023228786965,12.0,91.686,33,130.47123393300149
+11,20.0,107.27103402130513,,,3.0,137.6145750711021,8.0,96.67328958921384,31,130.66543582753627
+12,19.0,115.18484494064312,,,9.0,166.3941463513666,27.0,99.94044514609688,15,152.21269363624046
+13,8.0,115.92673350008616,,,4.0,167.8463882721341,18.0,112.46924027484135,11,156.91552993888146
+14,2.0,116.82938513918492,,,,,6.0,136.35409155577256,25,161.81013340331936
+15,4.0,117.55062463466538,,,,,41.0,165.7251932205843,13,169.13632057012472
+16,14.0,149.57199545369448,,,,,39.0,167.86077531097013,37,174.35990801786974
+17,12.0,170.03345068544604,,,,,3.0,197.68199389929276,26,192.21918426629537
+18,11.0,170.26763221469898,,,,,30.0,199.64515666551995,38,193.06534764167287
+19,5.0,180.93926111267285,,,,,,,36,193.95762797064725
+20,,,,,,,,,20,198.12128776080576
diff --git a/analysis_results/SNAP25/KO/with_segID/AZ_distances_within_40_with_diameters_and_seg_id.csv b/analysis_results/SNAP25/KO/with_segID/AZ_distances_within_40_with_diameters_and_seg_id.csv
new file mode 100644
index 0000000..6e9cb50
--- /dev/null
+++ b/analysis_results/SNAP25/KO/with_segID/AZ_distances_within_40_with_diameters_and_seg_id.csv
@@ -0,0 +1,6 @@
+,D_SNAP25_12.08.12_KO1.1_3_crop_seg_id,D_SNAP25_12.08.12_KO1.1_3_crop_distance,D_SNAP25_12.08.12_KO1.1_3_crop_diameter,C_SNAP25_12082_KO1.2_6_crop_seg_id,C_SNAP25_12082_KO1.2_6_crop_distance,C_SNAP25_12082_KO1.2_6_crop_diameter,E_SNAP25_12082_KO2.1_6_crop_seg_id,E_SNAP25_12082_KO2.1_6_crop_distance,E_SNAP25_12082_KO2.1_6_crop_diameter,A_SNAP25_12082_KO1.2_6_crop_seg_id,A_SNAP25_12082_KO1.2_6_crop_distance,A_SNAP25_12082_KO1.2_6_crop_diameter,B_SNAP25_12082_KO1.2_6_crop_seg_id,B_SNAP25_12082_KO1.2_6_crop_distance,B_SNAP25_12082_KO1.2_6_crop_diameter
+0,9,9.193587982936805,56.26909744547573,4,1.554,47.81289742868499,8,3.4748496370346733,54.5150906509724,13.0,4.662,49.91813042345726,1.0,6.216,62.88804789234515
+1,10,10.878,59.8139155734108,9,1.554,50.26043018499918,6,5.154034924212291,50.26043018499918,1.0,7.77,47.81289742868499,27.0,10.308069848424582,57.37547691442199
+2,13,12.90849348297469,62.34039118335815,7,4.662,46.96871937691663,11,6.216,58.36307916126143,9.0,9.452612972083434,46.96871937691663,,,
+3,15,14.660406679215962,49.91813042345726,8,6.216,57.37547691442199,12,6.407306142209845,56.26909744547573,11.0,11.419521180855176,51.49606651201725,,,
+4,18,22.46591738612069,64.59166755828387,5,13.636294658007358,51.71755599228722,14,6.407306142209845,57.37547691442199,,,,,,
diff --git a/analysis_results/SNAP25/KO/with_segID/AZ_distances_within_40_with_seg_id.csv b/analysis_results/SNAP25/KO/with_segID/AZ_distances_within_40_with_seg_id.csv
new file mode 100644
index 0000000..43211cc
--- /dev/null
+++ b/analysis_results/SNAP25/KO/with_segID/AZ_distances_within_40_with_seg_id.csv
@@ -0,0 +1,6 @@
+,D_SNAP25_12.08.12_KO1.1_3_crop_seg_id,D_SNAP25_12.08.12_KO1.1_3_crop_distance,C_SNAP25_12082_KO1.2_6_crop_seg_id,C_SNAP25_12082_KO1.2_6_crop_distance,E_SNAP25_12082_KO2.1_6_crop_seg_id,E_SNAP25_12082_KO2.1_6_crop_distance,A_SNAP25_12082_KO1.2_6_crop_seg_id,A_SNAP25_12082_KO1.2_6_crop_distance,B_SNAP25_12082_KO1.2_6_crop_seg_id,B_SNAP25_12082_KO1.2_6_crop_distance
+0,9,9.193587982936805,4,1.554,8,3.4748496370346733,13.0,4.662,1.0,6.216
+1,10,10.878,9,1.554,6,5.154034924212291,1.0,7.77,27.0,10.308069848424582
+2,13,12.90849348297469,7,4.662,11,6.216,9.0,9.452612972083434,,
+3,15,14.660406679215962,8,6.216,12,6.407306142209845,11.0,11.419521180855176,,
+4,18,22.46591738612069,5,13.636294658007358,14,6.407306142209845,,,,
diff --git a/scripts/cooper/run_compartment_segmentation.py b/scripts/cooper/run_compartment_segmentation.py
index 6396fd1..d4d3589 100644
--- a/scripts/cooper/run_compartment_segmentation.py
+++ b/scripts/cooper/run_compartment_segmentation.py
@@ -15,7 +15,7 @@ def run_compartment_segmentation(args):
         model_path = args.model
 
     segmentation_function = partial(
-        segment_compartments, model_path=model_path, verbose=False, tiling=tiling, scale=[0.25, 0.25, 0.25]
+        segment_compartments, model_path=model_path, verbose=False, tiling=tiling, scale=[0.25, 0.25, 0.25], boundary_threshold=args.boundary_threshold
     )
     inference_helper(
         args.input_path, args.output_path, segmentation_function, force=args.force, data_ext=args.data_ext
@@ -50,6 +50,9 @@ def main():
     parser.add_argument(
         "--data_ext", default=".mrc", help="The extension of the tomogram data. By default .mrc."
     )
+    parser.add_argument(
+        "--boundary_threshold", type=float, default=0.4, help="Threshold that determines when the prediction of the network is foreground for the segmentation. Need higher threshold than default for TEM."
+    )
 
     args = parser.parse_args()
     run_compartment_segmentation(args)
diff --git a/synapse_net/inference/compartments.py b/synapse_net/inference/compartments.py
index 0826827..113230f 100644
--- a/synapse_net/inference/compartments.py
+++ b/synapse_net/inference/compartments.py
@@ -155,6 +155,7 @@ def segment_compartments(
     scale: Optional[List[float]] = None,
     mask: Optional[np.ndarray] = None,
     n_slices_exclude: int = 0,
+    boundary_threshold: float=0.4,
     **kwargs,
 ) -> Union[np.ndarray, Tuple[np.ndarray, np.ndarray]]:
     """Segment synaptic compartments in an input volume.
@@ -168,6 +169,7 @@ def segment_compartments(
         return_predictions: Whether to return the predictions (foreground, boundaries) alongside the segmentation.
         scale: The scale factor to use for rescaling the input volume before prediction.
         n_slices_exclude:
+        boundary_threshold: Threshold that determines when the prediction of the network is foreground for the segmentation. Need higher threshold than default for TEM.
 
     Returns:
         The segmentation mask as a numpy array, or a tuple containing the segmentation mask
@@ -193,9 +195,9 @@ def segment_compartments(
     # We may want to expose some of the parameters here.
     t0 = time.time()
     if input_volume.ndim == 2:
-        seg = _segment_compartments_2d(pred)
+        seg = _segment_compartments_2d(pred, boundary_threshold=boundary_threshold)
     else:
-        seg = _segment_compartments_3d(pred, n_slices_exclude=n_slices_exclude)
+        seg = _segment_compartments_3d(pred, n_slices_exclude=n_slices_exclude, boundary_threshold=boundary_threshold)
     if verbose:
         print("Run segmentation in", time.time() - t0, "s")