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MariusCausemannMariusCausemann
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update config files to new scheme (without fixed)
1 parent b3f963c commit a9281af

10 files changed

Lines changed: 145 additions & 175 deletions

‎config_files/astrocyte1.yml‎

Lines changed: 9 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -1,17 +1,14 @@
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name : "astrocyte1"
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fixed :
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raw:
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cloudpath: "precomputed://gs://iarpa_microns/minnie/minnie65/seg"
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position : "189255-171091-22461" # http://tinyurl.com/ycytrm6t
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mip : 1
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processing:
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operation :
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- "ncells ncells=1 keep_cell_labels='[864691136194301772]'"
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- "smooth iterations=1 radius=2"
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- "erode radius=1"
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raw:
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size : [2500] #, 5000, 10000]
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cloudpath: "precomputed://gs://iarpa_microns/minnie/minnie65/seg"
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position : "189255-171091-22461" # http://tinyurl.com/ycytrm6t
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mip : 1
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size : 2500
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processing:
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dx : 20
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meshing:
9+
operation :
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- "ncells ncells=1 keep_cell_labels='[864691136194301772]'"
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- "smooth iterations=1 radius=2"
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- "erode radius=1"
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meshing:
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envelopsize : [8]

‎config_files/cappilary1.yml‎

Lines changed: 17 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -1,26 +1,23 @@
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name : "cappilary1"
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fixed :
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raw:
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cloudpath: "precomputed://gs://iarpa_microns/minnie/minnie65/seg"
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position : "232915-165336-20525"
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processing:
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operation :
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- "merge labels='[864691136534887842,864691135476973891,864691135751005697,864691133070457251,864691136178683094,864691133070456483,864691133070450083,864691133003757151,864691136475845441,864691134032036203,864691131901467286]'"
9-
- "dilate radius=4 labels='[864691134581644554,864691135228370458,864691135918336944,864691136475874625,864691136723365629,864691134308859492]'"
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- "removeislands minsize=5000"
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- "dilate radius=5"
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- "smooth iterations=2 radius=4"
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- "erode radius=1"
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- "roigenerate labels='[864691136534887842]'"
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- "roidilate radius=80"
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- "roiapply"
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- "erode radius=15 labels='[864691136534887842]'"
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- "removeislands minsize=5000"
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- "roierode radius=4"
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raw:
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cloudpath: "precomputed://gs://iarpa_microns/minnie/minnie65/seg"
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position : "232915-165336-20525"
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mip : 0
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size : [7500]
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size : 7500
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processing:
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dx : 8
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operation :
10+
- "merge labels='[864691136534887842,864691135476973891,864691135751005697,864691133070457251,864691136178683094,864691133070456483,864691133070450083,864691133003757151,864691136475845441,864691134032036203,864691131901467286]'"
11+
- "dilate radius=4 labels='[864691134581644554,864691135228370458,864691135918336944,864691136475874625,864691136723365629,864691134308859492]'"
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- "removeislands minsize=5000"
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- "dilate radius=5"
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- "smooth iterations=2 radius=4"
15+
- "erode radius=1"
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- "roigenerate labels='[864691136534887842]'"
17+
- "roidilate radius=80"
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- "roiapply"
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- "erode radius=15 labels='[864691136534887842]'"
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- "removeislands minsize=5000"
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- "roierode radius=4"
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meshing:
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envelopsize : [5]
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envelopsize : 5

‎config_files/cappilary2.yml‎

Lines changed: 17 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -1,26 +1,23 @@
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name : "cappilary2"
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fixed :
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raw:
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cloudpath: "precomputed://gs://iarpa_microns/minnie/minnie65/seg"
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position : "337400-138900-22519"
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processing:
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operation:
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- "merge labels='[864691136534887842,864691133995183345,864691134924323841,864691135197974302,864691135501607490,864691135686365079,864691135954940163,864691132805951425,864691132361462832,864691132805954753,864691132805951681,864691134924324353,864691132805952961,864691132805951169]'"
9-
- "dilate radius=4 labels='[864691135211452360,864691135212672968,864691135213024712,864691135592508823,864691136215403699]'"
10-
- "removeislands minsize=5000"
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- "dilate radius=5"
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- "smooth iterations=2 radius=4"
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- "erode radius=1"
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- "roigenerate labels='[864691136534887842]'"
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- "roidilate radius=64"
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- "roiapply"
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- "erode radius=15 labels='[864691136534887842]'"
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- "removeislands minsize=5000"
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- "roierode radius=4"
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raw:
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cloudpath: "precomputed://gs://iarpa_microns/minnie/minnie65/seg"
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position : "337400-138900-22519"
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mip : 0
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size : [7500]
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size : 7500
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processing:
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dx : 8
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operation:
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- "merge labels='[864691136534887842,864691133995183345,864691134924323841,864691135197974302,864691135501607490,864691135686365079,864691135954940163,864691132805951425,864691132361462832,864691132805954753,864691132805951681,864691134924324353,864691132805952961,864691132805951169]'"
11+
- "dilate radius=4 labels='[864691135211452360,864691135212672968,864691135213024712,864691135592508823,864691136215403699]'"
12+
- "removeislands minsize=5000"
13+
- "dilate radius=5"
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- "smooth iterations=2 radius=4"
15+
- "erode radius=1"
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- "roigenerate labels='[864691136534887842]'"
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- "roidilate radius=64"
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- "roiapply"
19+
- "erode radius=15 labels='[864691136534887842]'"
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- "removeislands minsize=5000"
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- "roierode radius=4"
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meshing:
26-
envelopsize : [5]
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envelopsize : 5

‎config_files/cappilary3.yml‎

Lines changed: 16 additions & 19 deletions
Original file line numberDiff line numberDiff line change
@@ -1,25 +1,22 @@
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name : "cappilary3"
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fixed :
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raw:
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cloudpath: "precomputed://gs://iarpa_microns/minnie/minnie65/seg"
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position : "307339-124630-24240"
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processing:
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operation :
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- "merge labels='[864691136534887842,864691135941292148,864691132616222812]'"
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- "removeislands minsize=5000"
10-
- "dilate radius=5"
11-
- "smooth iterations=2 radius=4"
12-
- "erode radius=1"
13-
- "roigenerate labels='[864691136534887842]'"
14-
- "roidilate radius=64"
15-
- "roiapply"
16-
- "erode radius=15 labels='[864691136534887842]'"
17-
- "removeislands minsize=5000"
18-
- "roierode radius=4"
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raw:
3+
cloudpath: "precomputed://gs://iarpa_microns/minnie/minnie65/seg"
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position : "307339-124630-24240"
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mip : 0
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size : [7500]
227
processing:
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dx : 8
8+
dx : 8
9+
operation :
10+
- "merge labels='[864691136534887842,864691135941292148,864691132616222812]'"
11+
- "removeislands minsize=5000"
12+
- "dilate radius=5"
13+
- "smooth iterations=2 radius=4"
14+
- "erode radius=1"
15+
- "roigenerate labels='[864691136534887842]'"
16+
- "roidilate radius=64"
17+
- "roiapply"
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- "erode radius=15 labels='[864691136534887842]'"
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- "removeislands minsize=5000"
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- "roierode radius=4"
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meshing:
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envelopsize : [5]
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envelopsize : 5

‎config_files/cappilary4.yml‎

Lines changed: 16 additions & 19 deletions
Original file line numberDiff line numberDiff line change
@@ -1,25 +1,22 @@
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name : "cappilary4"
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fixed :
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raw:
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cloudpath: "precomputed://gs://iarpa_microns/minnie/minnie65/seg"
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position : "306009-143434-23494"
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processing:
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operation :
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- "merge labels='[864691136534887842,864691133311938372,864691133711003153,864691135468246461]'"
9-
- "removeislands minsize=5000"
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- "dilate radius=5"
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- "smooth iterations=2 radius=4"
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- "erode radius=1"
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- "roigenerate labels='[864691136534887842]'"
14-
- "roidilate radius=64"
15-
- "roiapply"
16-
- "erode radius=15 labels='[864691136534887842]'"
17-
- "removeislands minsize=5000"
18-
- "roierode radius=4"
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raw:
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cloudpath: "precomputed://gs://iarpa_microns/minnie/minnie65/seg"
4+
position : "306009-143434-23494"
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mip : 0
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size : [7500]
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size : 7500
227
processing:
238
dx : 8
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operation :
10+
- "merge labels='[864691136534887842,864691133311938372,864691133711003153,864691135468246461]'"
11+
- "removeislands minsize=5000"
12+
- "dilate radius=5"
13+
- "smooth iterations=2 radius=4"
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- "erode radius=1"
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- "roigenerate labels='[864691136534887842]'"
16+
- "roidilate radius=64"
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- "roiapply"
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- "erode radius=15 labels='[864691136534887842]'"
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- "removeislands minsize=5000"
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- "roierode radius=4"
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meshing:
25-
envelopsize : [5]
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envelopsize : 5

‎config_files/cappilary5.yml‎

Lines changed: 16 additions & 19 deletions
Original file line numberDiff line numberDiff line change
@@ -1,25 +1,22 @@
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name : "cappilary5"
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fixed :
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raw:
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cloudpath: "precomputed://gs://iarpa_microns/minnie/minnie65/seg"
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position : "232042-166129-21467"
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processing:
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operation :
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- "merge labels='[864691136534887842,864691132131484059,864691132336155009,864691132348210676,864691135791214365,864691135971392446]'"
9-
- "removeislands minsize=5000"
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- "dilate radius=5"
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- "smooth iterations=2 radius=4"
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- "erode radius=1"
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- "roigenerate labels='[864691136534887842]'"
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- "roidilate radius=64"
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- "roiapply"
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- "erode radius=15 labels='[864691136534887842]'"
17-
- "removeislands minsize=5000"
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- "roierode radius=4"
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raw:
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cloudpath: "precomputed://gs://iarpa_microns/minnie/minnie65/seg"
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position : "232042-166129-21467"
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mip : 0
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size : [7500]
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size : 7500
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processing:
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dx : 8
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operation :
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- "merge labels='[864691136534887842,864691132131484059,864691132336155009,864691132348210676,864691135791214365,864691135971392446]'"
11+
- "removeislands minsize=5000"
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- "dilate radius=5"
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- "smooth iterations=2 radius=4"
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- "erode radius=1"
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- "roigenerate labels='[864691136534887842]'"
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- "roidilate radius=64"
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- "roiapply"
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- "erode radius=15 labels='[864691136534887842]'"
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- "removeislands minsize=5000"
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- "roierode radius=4"
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meshing:
25-
envelopsize : [5]
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envelopsize : 5

‎config_files/cappilary6.yml‎

Lines changed: 16 additions & 19 deletions
Original file line numberDiff line numberDiff line change
@@ -1,26 +1,23 @@
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name : "cappilary6"
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fixed :
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raw:
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cloudpath: "precomputed://gs://iarpa_microns/minnie/minnie65/seg"
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position : "230671-173653-22233"
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processing:
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operation :
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- "merge labels='[864691136534887842,864691135776576352,864691135807087133]'"
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- "dilate radius=4 labels='[864691135000029429,864691135000202997,864691135609682183,864691135855609134]'"
10-
- "removeislands minsize=5000"
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- "dilate radius=5"
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- "smooth iterations=2 radius=4"
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- "erode radius=1"
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- "roigenerate labels='[864691136534887842]'"
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- "roidilate radius=80"
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- "roiapply"
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- "erode radius=15 labels='[864691136534887842]'"
18-
- "removeislands minsize=5000"
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- "roierode radius=4"
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raw:
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cloudpath: "precomputed://gs://iarpa_microns/minnie/minnie65/seg"
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position : "230671-173653-22233"
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mip : 0
226
size : [7500]
237
processing:
248
dx : 8
9+
operation :
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- "merge labels='[864691136534887842,864691135776576352,864691135807087133]'"
11+
- "dilate radius=4 labels='[864691135000029429,864691135000202997,864691135609682183,864691135855609134]'"
12+
- "removeislands minsize=5000"
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- "dilate radius=5"
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- "smooth iterations=2 radius=4"
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- "erode radius=1"
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- "roigenerate labels='[864691136534887842]'"
17+
- "roidilate radius=80"
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- "roiapply"
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- "erode radius=15 labels='[864691136534887842]'"
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- "removeislands minsize=5000"
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- "roierode radius=4"
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meshing:
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envelopsize : [5]
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envelopsize : 5

‎config_files/cappilary7.yml‎

Lines changed: 16 additions & 19 deletions
Original file line numberDiff line numberDiff line change
@@ -1,26 +1,23 @@
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name : "cappilary7"
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fixed :
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raw:
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cloudpath: "precomputed://gs://iarpa_microns/minnie/minnie65/seg"
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position : "257957-186674-20614" #https://tinyurl.com/3smjnb4m
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processing:
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operation :
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- "merge labels='[864691136534887842,864691135662897092,864691132540602862]'"
9-
- "dilate radius=4 labels='[864691135097319093,864691135097324469,864691135181838082,864691135472006194,864691135777250237,864691136194177256]'"
10-
- "removeislands minsize=5000"
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- "dilate radius=5"
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- "smooth iterations=2 radius=4"
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- "erode radius=2"
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- "roigenerate labels='[864691136534887842]'"
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- "roidilate radius=64"
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- "roiapply"
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- "erode radius=15 labels='[864691136534887842]'"
18-
- "removeislands minsize=5000"
19-
- "roierode radius=4"
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raw:
3+
cloudpath: "precomputed://gs://iarpa_microns/minnie/minnie65/seg"
4+
position : "257957-186674-20614" #https://tinyurl.com/3smjnb4m
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mip : 0
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size : "7500-7500-5000"
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processing:
248
dx : 8
9+
operation :
10+
- "merge labels='[864691136534887842,864691135662897092,864691132540602862]'"
11+
- "dilate radius=4 labels='[864691135097319093,864691135097324469,864691135181838082,864691135472006194,864691135777250237,864691136194177256]'"
12+
- "removeislands minsize=5000"
13+
- "dilate radius=5"
14+
- "smooth iterations=2 radius=4"
15+
- "erode radius=2"
16+
- "roigenerate labels='[864691136534887842]'"
17+
- "roidilate radius=64"
18+
- "roiapply"
19+
- "erode radius=15 labels='[864691136534887842]'"
20+
- "removeislands minsize=5000"
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- "roierode radius=4"
2522
meshing:
26-
envelopsize : [8]
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envelopsize : 8

‎config_files/cortical_mm3.yml‎

Lines changed: 13 additions & 16 deletions
Original file line numberDiff line numberDiff line change
@@ -1,20 +1,17 @@
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name : cortical_mm3
2-
fixed :
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raw:
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cloudpath : "precomputed://gs://iarpa_microns/minnie/minnie65/seg"
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mip : 2
6-
position : "225182-107314-22000"
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processing:
8-
operation :
9-
- "removeislands minsize=5000"
10-
- "dilate radius=1"
11-
- "smooth iterations=1 radius=1"
12-
- "erode radius=1"
13-
- "removeislands minsize=5000"
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raw:
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size : [10000] #[5000, 10000, 20000]
16-
processing:
3+
cloudpath : "precomputed://gs://iarpa_microns/minnie/minnie65/seg"
4+
mip : 2
5+
position : "225182-107314-22000"
6+
size : 10000
7+
processing:
178
dx : 20
18-
ncells : [10] #[5, 50, 200, 500]
9+
ncells : 10
10+
operation :
11+
- "removeislands minsize=5000"
12+
- "dilate radius=1"
13+
- "smooth iterations=1 radius=1"
14+
- "erode radius=1"
15+
- "removeislands minsize=5000"
1916
meshing:
20-
envelopsize : [18]
17+
envelopsize : 18

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