Replace pyclesperanto with nbmorph

.github/workflows/test_conda.yml

@@ -16,20 +16,23 @@ defaults:
 
 jobs:
   test_scripts:
-    runs-on: ubuntu-latest
-    container: ubuntu:latest
+    name: test on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-15-intel, macos-15]
+
 
     steps:
       - uses: actions/checkout@v4
 
-      #   - uses: actions/setup-python@v5
-      #     with:
-      #       python-version: "3.11"
-      - name: Install deps
+      - name: Install Headless Plotting Libs
+        if: runner.os == 'Linux'
         run: |
-          DEBIAN_FRONTEND=noninteractive apt-get update
-          DEBIAN_FRONTEND=noninteractive apt-get install -y gcc unzip make cmake build-essential git libgmp-dev xvfb intel-opencl-icd pocl-opencl-icd
-      #       python -m pip install snakemake
+          sudo apt-get update
+          sudo apt-get install -y libosmesa6 libgl1
+
       - name: Setup conda-forge
         uses: conda-incubator/setup-miniconda@v3
         with:
@@ -43,4 +46,4 @@ jobs:
           conda install snakemake snakemake-storage-plugin-http snakemake-executor-plugin-cluster-generic
       - name: Run snakemake
         run: |
-          export PYOPENCL_COMPILER_OUTPUT=1 && snakemake --use-conda --cores 2 -p --configfile ./config_files/test.yml
+          snakemake --use-conda --cores 2 -p --configfile ./config_files/test.yml

.gitignore

@@ -8,4 +8,5 @@ fTetWild
 zipped
 zipped_surf
 .snakemake
-.vscode
+.vscode
+.cache

config_files/astrocyte1.yml

@@ -3,17 +3,15 @@ fixed :
   raw:
     cloudpath: "precomputed://gs://iarpa_microns/minnie/minnie65/seg"
     position : "189255-171091-22461" # http://tinyurl.com/ycytrm6t
+    mip : 1
   processing:
-      cells : 864691136194301772
+      operation : 
+        - "ncells ncells=1 keep_cell_labels='[864691136194301772]'"
+        - "smooth iterations=1 radius=2"
+        - "erode radius=1"
 raw:
-  mip : 1
-  size : [2500, 5000, 10000] 
+  size : [2500] #, 5000, 10000] 
 processing:
-  ncells : [ 1 ]
-  smoothiter : [1]
-  smoothradius : [2]
-  expand : [1]
-  shrink : 0
   dx : 20
 meshing:
   envelopsize : [8]

config_files/cappilary1.yml

@@ -4,22 +4,19 @@ fixed :
     cloudpath: "precomputed://gs://iarpa_microns/minnie/minnie65/seg"
     position : "232915-165336-20525"
   processing:
-    #roi : 864691136534887842
-    #merge :  864691136534887842 864691135476973891 864691135751005697 864691133070457251 864691136178683094 864691133070456483 864691133070450083 864691133003757151 864691136475845441 864691134032036203
-    #cells : 864691134581644554 864691135228370458 864691135918336944 864691136475874625 864691136723365629
     operation : 
       - "merge labels='[864691136534887842, 864691135476973891, 864691135751005697, 864691133070457251, 864691136178683094, 864691133070456483, 864691133070450083, 864691133003757151, 864691136475845441, 864691134032036203, 864691131901467286]'"
-      - "dilate iterations=2 radius=2 labels='[864691134581644554, 864691135228370458, 864691135918336944, 864691136475874625, 864691136723365629, 864691134308859492]'"
+      - "dilate radius=4 labels='[864691134581644554, 864691135228370458, 864691135918336944, 864691136475874625, 864691136723365629, 864691134308859492]'"
       - "removeislands minsize=5000"
-      - "dilate iterations=3 radius=3"
-      - "smooth iterations=3 radius=5"
-      - "erode iterations=1 radius=1"
+      - "dilate radius=5"
+      - "smooth iterations=2 radius=4"
+      - "erode radius=1"
       - "roigenerate labels='[864691136534887842]'"
-      - "roidilate iterations=10 radius=8"
+      - "roidilate radius=80"
       - "roiapply"
-      - "erode iterations=3 radius=5 labels='[864691136534887842]'"
+      - "erode radius=15 labels='[864691136534887842]'"
       - "removeislands minsize=5000"
-      - "roierode iterations=2 radius=2"
+      - "roierode radius=4"
 raw:
   mip : 0
   size : [7500] 

config_files/cappilary2.yml

@@ -4,19 +4,23 @@ fixed :
     cloudpath: "precomputed://gs://iarpa_microns/minnie/minnie65/seg"
     position : "337400-138900-22519"
   processing:
-    roi : 864691136534887842
-    merge : "864691136534887842 864691133995183345 864691134924323841 864691135197974302 864691135501607490 864691135686365079 864691135954940163 864691132805951425 864691132361462832 864691132805954753 864691132805951681 864691134924324353 864691132805952961 864691132805951169"
-    cells : 864691135211452360 864691135212672968 864691135213024712  864691135592508823 864691136215403699 #864691133186201551
+    operation:
+      - "merge labels='[864691136534887842, 864691133995183345, 864691134924323841, 864691135197974302, 864691135501607490, 864691135686365079, 864691135954940163, 864691132805951425, 864691132361462832, 864691132805954753, 864691132805951681, 864691134924324353, 864691132805952961, 864691132805951169]'"
+      - "dilate radius=4 labels='[864691135211452360, 864691135212672968, 864691135213024712,  864691135592508823, 864691136215403699]'"
+      - "removeislands minsize=5000"
+      - "dilate radius=5"
+      - "smooth iterations=2 radius=4"
+      - "erode radius=1"
+      - "roigenerate labels='[864691136534887842]'"
+      - "roidilate radius=64"
+      - "roiapply"
+      - "erode radius=15 labels='[864691136534887842]'"
+      - "removeislands minsize=5000"
+      - "roierode radius=4"
 raw:
-  mip : 1
+  mip : 0
   size : [7500] 
 processing:
-  ncells : [ 1000 ]
-  smoothiter : [3]
-  smoothradius : [3]
-  expand : [3]
-  shrink : 1
-  dx : 20
-  roidilate: "6-6"
+  dx : 8
 meshing:
-  envelopsize : [8]
+  envelopsize : [5]

config_files/cappilary3.yml

@@ -4,18 +4,22 @@ fixed :
     cloudpath: "precomputed://gs://iarpa_microns/minnie/minnie65/seg"
     position : "307339-124630-24240"
   processing:
-    roi : 864691136534887842
-    merge : "864691136534887842 864691135941292148 864691132616222812" # 864691135322955164"
+      operation : 
+      - "merge labels='[864691136534887842, 864691135941292148, 864691132616222812]'"
+      - "removeislands minsize=5000"
+      - "dilate radius=5"
+      - "smooth iterations=2 radius=4"
+      - "erode radius=1"
+      - "roigenerate labels='[864691136534887842]'"
+      - "roidilate radius=64"
+      - "roiapply"
+      - "erode radius=15 labels='[864691136534887842]'"
+      - "removeislands minsize=5000"
+      - "roierode radius=4"
 raw:
-  mip : 1
+  mip : 0
   size : [7500] 
 processing:
-  ncells : [ 1000 ]
-  smoothiter : [3]
-  smoothradius : [3]
-  expand : [3]
-  shrink : 1
-  dx : 20
-  roidilate: "6-6"
+  dx : 8
 meshing:
-  envelopsize : [8]
+  envelopsize : [5]

config_files/cappilary4.yml

@@ -4,18 +4,22 @@ fixed :
     cloudpath: "precomputed://gs://iarpa_microns/minnie/minnie65/seg"
     position : "306009-143434-23494"
   processing:
-    roi : 864691136534887842
-    merge : "864691136534887842 864691133311938372 864691133711003153 864691135468246461" #864691132824819233 864691133334749831
+    operation : 
+      - "merge labels='[864691136534887842, 864691133311938372, 864691133711003153, 864691135468246461]'"
+      - "removeislands minsize=5000"
+      - "dilate radius=5"
+      - "smooth iterations=2 radius=4"
+      - "erode radius=1"
+      - "roigenerate labels='[864691136534887842]'"
+      - "roidilate radius=64"
+      - "roiapply"
+      - "erode radius=15 labels='[864691136534887842]'"
+      - "removeislands minsize=5000"
+      - "roierode radius=4"
 raw:
-  mip : 1
+  mip : 0
   size : [7500] 
 processing:
-  ncells : [ 1000 ]
-  smoothiter : [3]
-  smoothradius : [3]
-  expand : [3]
-  shrink : 1
-  dx : 20
-  roidilate: "6-6"
+  dx : 8
 meshing:
-  envelopsize : [8]
+  envelopsize : [5]

config_files/cappilary5.yml

@@ -4,19 +4,18 @@ fixed :
     cloudpath: "precomputed://gs://iarpa_microns/minnie/minnie65/seg"
     position : "232042-166129-21467"
   processing:
-    #cells : 864691132723008555 864691134309135460 864691134310007140 864691135609682183 864691135753683149 864691135918336944
     operation : 
       - "merge labels='[864691136534887842, 864691132131484059, 864691132336155009, 864691132348210676, 864691135791214365, 864691135971392446]'"
       - "removeislands minsize=5000"
-      - "dilate iterations=3 radius=3"
-      - "smooth iterations=3 radius=5"
-      - "erode iterations=1 radius=1"
+      - "dilate radius=5"
+      - "smooth iterations=2 radius=4"
+      - "erode radius=1"
       - "roigenerate labels='[864691136534887842]'"
-      - "roidilate iterations=8 radius=8"
+      - "roidilate radius=64"
       - "roiapply"
-      - "erode iterations=3 radius=5 labels='[864691136534887842]'"
+      - "erode radius=15 labels='[864691136534887842]'"
       - "removeislands minsize=5000"
-      - "roierode iterations=2 radius=2"
+      - "roierode radius=4"
 raw:
   mip : 0
   size : [7500] 

config_files/cappilary6.yml

@@ -4,19 +4,23 @@ fixed :
     cloudpath: "precomputed://gs://iarpa_microns/minnie/minnie65/seg"
     position : "230671-173653-22233"
   processing:
-    roi : 864691136534887842
-    merge : 864691135776576352 864691135807087133 864691136534887842
-    cells : 864691135000029429 864691135000202997 864691135609682183 864691135855609134
+    operation : 
+      - "merge labels='[864691136534887842, 864691135776576352, 864691135807087133]'"
+      - "dilate radius=4 labels='[864691135000029429, 864691135000202997, 864691135609682183, 864691135855609134]'"
+      - "removeislands minsize=5000"
+      - "dilate radius=5"
+      - "smooth iterations=2 radius=4"
+      - "erode radius=1"
+      - "roigenerate labels='[864691136534887842]'"
+      - "roidilate radius=80"
+      - "roiapply"
+      - "erode radius=15 labels='[864691136534887842]'"
+      - "removeislands minsize=5000"
+      - "roierode radius=4"
 raw:
   mip : 0
   size : [7500] 
 processing:
-  ncells : [ 1000 ]
-  smoothiter : [3]
-  smoothradius : [3]
-  expand : [3]
-  shrink : 1
   dx : 8
-  roidilate: "8-8"
 meshing:
-  envelopsize : [8]
+  envelopsize : [5]

config_files/cappilary7.yml

@@ -6,17 +6,17 @@ fixed :
   processing:
     operation : 
       - "merge labels='[864691136534887842, 864691135662897092, 864691132540602862]'"
-      - "dilate iterations=2 radius=2 labels='[864691135097319093, 864691135097324469, 864691135181838082, 864691135472006194, 864691135777250237, 864691136194177256]'"
+      - "dilate radius=4 labels='[864691135097319093, 864691135097324469, 864691135181838082, 864691135472006194, 864691135777250237, 864691136194177256]'"
       - "removeislands minsize=5000"
-      - "dilate iterations=3 radius=3"
-      - "smooth iterations=3 radius=5"
-      - "erode iterations=2 radius=1"
+      - "dilate radius=5"
+      - "smooth iterations=2 radius=4"
+      - "erode radius=2"
       - "roigenerate labels='[864691136534887842]'"
-      - "roidilate iterations=8 radius=8"
+      - "roidilate radius=64"
       - "roiapply"
-      - "erode iterations=3 radius=5 labels='[864691136534887842]'"
+      - "erode radius=15 labels='[864691136534887842]'"
       - "removeislands minsize=5000"
-      - "roierode iterations=2 radius=2"
+      - "roierode radius=4"
 raw:
   mip : 0
   size : "7500-7500-5000"

config_files/cortical_mm3.yml

@@ -7,14 +7,14 @@ fixed :
   processing:
     operation : 
       - "removeislands minsize=5000"
-      - "dilate iterations=1 radius=1"
+      - "dilate radius=1"
       - "smooth iterations=1 radius=1"
-      - "erode iterations=1 radius=1"
+      - "erode radius=1"
       - "removeislands minsize=5000"
 raw:
-  size : [5000, 10000, 20000, 40000,]
+  size : [10000] #[5000, 10000, 20000]
 processing: 
   dx : 20
-  ncells : [5, 10, 50, 100, 200, 500, 1000]
+  ncells : [10] #[5,  50, 200, 500]
 meshing:
   envelopsize : [18]

config_files/motta2019.yml

@@ -1,12 +1,19 @@
-dataset : "motta"
-cloudpath : 
-  "motta": "https://webknossos.org/datasets/MPI_Brain_Research/2012-09-28_ex145_07x2_ROI2017_connectome/view/"
-mip : [2]
-position : "2016-3595-2015"
-size : [5000, 10000, 20000] 
-ncells : [5, 10, 50, 100, 200, 1000]
-smoothiter : [0,]
-smoothradius : 0
-expand : [0]
-shrink : 0
-envelopsize : [8]
+name : "motta2019"
+fixed : 
+  raw:
+    cloudpath: "https://webknossos.org/datasets/l4dense_motta_et_al_demo-5f33d5340100001800e8cddc/view"
+    position : "2816-4352-1792"
+  processing:
+    operation : 
+      - "removeislands minsize=8000"
+      - "dilate radius=1"
+      - "smooth iterations=3 radius=6"
+      - "erode radius=3"
+raw:
+  mip : 2
+  size : [4000] 
+processing:
+  dx : 18
+meshing:
+  envelopsize : [12]
+

config_files/test.yml

@@ -2,24 +2,23 @@ name : "test"
 fixed : 
   raw:
     cloudpath: "precomputed://gs://iarpa_microns/minnie/minnie65/seg"
-    position : "232042-166129-21467"
+    position : "232000-166129-21467"
   processing:
-    #cells : 864691132723008555 864691134309135460 864691134310007140 864691135609682183 864691135753683149 864691135918336944
     operation : 
       - "merge labels='[864691136534887842, 864691132131484059, 864691132336155009, 864691132348210676, 864691135791214365, 864691135971392446]'"
       - "removeislands minsize=5000"
-      - "dilate iterations=3 radius=3"
-      - "smooth iterations=3 radius=5"
-      - "erode iterations=1 radius=1"
+      - "dilate radius=5"
+      - "smooth iterations=2 radius=4"
+      - "erode radius=1"
       - "roigenerate labels='[864691136534887842]'"
-      - "roidilate iterations=4 radius=6"
+      - "roidilate radius=24"
       - "roiapply"
-      - "erode iterations=3 radius=5 labels='[864691136534887842]'"
+      - "erode radius=15 labels='[864691136534887842]'"
       - "removeislands minsize=5000"
-      - "roierode iterations=2 radius=1"
+      - "roierode radius=2"
 raw:
   mip : 1
-  size : [5000] 
+  size : [7000] 
 processing:
   dx : 18
 meshing: