add JRCFIB2022M template + mesh + transform to FAFB14

navis-org · May 20, 2022 · ddf686c · ddf686c
1 parent ef1d7c2
commit ddf686c
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Showing 6 changed files with 154 additions and 3 deletions.
diff --git a/flybrains/core.py b/flybrains/core.py
@@ -392,6 +392,28 @@ def register_transforms():
                                            target='FANCnm',
                                            transform_type='bridging')
 
+    # Add a male CNS <-> FAFB transform
+    fp = os.path.join(data_filepath, 'maleCNS_brain_FAFB_landmarks_nm.csv')
+    lm = pd.read_csv(fp)
+    tr = transforms.TPStransform(lm[['fafb_x', 'fafb_y', 'fafb_z']].values,
+                                 lm[['cns_x', 'cns_y', 'cns_z']].values)
+    transforms.registry.register_transform(transform=tr,
+                                           source='FAFB14',
+                                           target='JRCFIB2022M',
+                                           transform_type='bridging')
+    tr = transforms.AliasTransform()
+    transforms.registry.register_transform(transform=tr,
+                                           source='JRCFIB2022M',
+                                           target='JRCFIB2022Mnm',
+                                           transform_type='bridging')
+
+    # Add transform between voxel and nm space
+    tr = transforms.AffineTransform(np.diag([8, 8, 8, 1]))
+    transforms.registry.register_transform(transform=tr,
+                                           source='JRCFIB2022Mraw',
+                                           target='JRCFIB2022M',
+                                           transform_type='bridging')
+
     # Add FANC mirror transform based on subsampling a FANC -> MANCsym transform
     fp = os.path.join(data_filepath, 'FANC_mirror_landmarks.csv')
     lm = pd.read_csv(fp)

diff --git a/flybrains/data/README.md b/flybrains/data/README.md
@@ -58,6 +58,13 @@ male adult nerve cord (MANC) and female adult nerve cord (FANC) VNC data sets.
 These landmarks were manually placed at cross-identifiable locations in both
 datasets.
 
+## `maleCNS_brain_FAFB_landmarks_um.csv`
+This file contains landmarks to transform between the brain portion of the
+Janelia full male CNS and the FAFB datasets.
+
+These landmarks were manually placed using the Big Warp on the images created
+from synapse clouds.
+
 # Transforms
 
 ## `TransformParameters.FixedFANC.txt` & TransformParameters.FixedTemplate.txt

diff --git a/flybrains/data/maleCNS_brain_FAFB_landmarks_nm.csv b/flybrains/data/maleCNS_brain_FAFB_landmarks_nm.csv
@@ -0,0 +1,70 @@
+,fafb_x,fafb_y,fafb_z,cns_x,cns_y,cns_z
+0,522329,183049,95207,388026,161159,167533
+1,454391,88801,95359,316430,61913,170284
+2,597492,98038,83202,448916,60418,171139
+3,520008,210975,125015,386935,193888,208371
+4,414541,169814,155265,274930,152795,222699
+5,645532,176758,134322,501849,141522,219899
+6,524189,343058,129754,390374,358625,202136
+7,527478,343058,164366,391470,346564,250637
+8,433912,304681,164622,300097,308187,240842
+9,622141,309798,150989,482113,296857,235944
+10,580109,264476,150733,435695,246053,240622
+11,471192,256436,153474,345784,253363,241134
+12,402081,199131,89578,264353,182932,151045
+13,641845,213019,59242,515372,176609,140441
+14,587752,290138,62130,454442,261756,139151
+15,460560,279174,76420,330067,276755,143621
+16,510633,223619,82305,370272,205483,151954
+17,548279,230563,68087,411207,200001,151369
+18,742267,193022,218409,613704,156201,309726
+19,317205,191683,251306,170238,167008,319930
+20,370865,321156,190040,238191,335991,270355
+21,686426,350570,176597,540117,336062,288892
+22,493283,217407,29135,351336,200430,107763
+23,467762,236328,26538,335051,226704,100604
+24,562985,183709,93767,424379,159948,169974
+25,484582,178909,102087,350456,161269,170502
+26,659068,252752,139167,517314,233231,231104
+27,391889,245008,157899,257423,232268,230181
+28,392373,158852,104124,245230,144815,158189
+29,661928,173900,68394,535159,136103,157802
+30,682504,237242,91421,551394,202480,180216
+31,362170,227121,125787,227126,211720,187145
+32,276261,150971,214870,145390,118634,266812
+33,770671,161627,170025,630291,107194,266812
+34,732191,346868,206023,581449,350964,303510
+35,845190,277803,209271,723165,260378,294788
+36,266984,308774,262709,120778,336502,334874
+37,699473,150054,159934,549683,107246,243727
+38,677974,149896,82227,535602,100206,171080
+39,637337,155401,45932,508321,126607,131346
+40,662619,251891,44177,532962,207130,136274
+41,383399,232165,77052,251119,219890,140485
+42,419929,92468,163797,279280,51803,235661
+43,726375,183387,194529,585219,141878,283603
+44,298769,162288,224807,157845,138117,286167
+45,299516,372896,212310,168102,411209,293433
+46,433202,221557,40881,289476,211369,114363
+47,516617,231926,52162,370677,210472,129321
+48,444852,195253,44243,306571,178248,117355
+49,474205,337062,71571,352727,339410,143852
+50,564274,344863,56718,421535,338086,157100
+51,522742,354271,125930,392046,362916,199838
+52,555476,285496,79250,417261,265987,156246
+53,622562,265970,52918,488205,228891,131031
+54,668613,289834,79328,535644,261756,166930
+55,596927,324671,76043,464272,310392,167357
+56,350350,244326,149923,212976,232268,222061
+57,343448,338601,227556,205283,361933,312665
+58,504969,144276,161661,362557,126364,236165
+59,559057,149457,156551,410423,122304,237874
+60,531155,171133,164516,387345,146109,251123
+61,544699,129111,63252,405324,103572,133483
+62,500821,126569,66751,365481,105716,127501
+63,618856,228596,23059,474349,190599,99596
+64,561174,272361,22491,424774,237054,102588
+65,545274,234874,37355,417226,203831,123956
+66,608330,211789,30053,463574,168778,106861
+67,617084,220714,71798,487042,174379,142684
+68,607961,176996,51981,470064,151746,124165
diff --git a/flybrains/data/template_meta.json b/flybrains/data/template_meta.json
@@ -573,6 +573,34 @@
       "description": "Uncalibrated version of Janelia FIB hemibrain dataset",
       "doi": "https://doi.org/10.1101/2020.01.21.911859"
    },
+   {
+      "name": "JRCFIB2022M",
+      "label": "JRCFIB2022M",
+      "type": null,
+      "sex": "M",
+      "dims": [
+        94088,
+        71047,
+        60858
+      ],
+      "voxdims": [
+         8,
+         8,
+         8
+      ],
+      "origin": null,
+      "boundingbox": [
+         0,
+         752704,
+         0,
+         568376,
+         0,
+         484680
+      ],
+      "units": "nanometers",
+      "description": "Full male CNS EM volume currenty being generated by FlyEM at HHMI Janelia Research Campus",
+      "doi": "unpublished"
+   },
    {
       "name": "JRCVNC2018F",
       "label": "JRCVNC2018F",

diff --git a/flybrains/meshes/JRCFIB2022M.ply b/flybrains/meshes/JRCFIB2022M.ply
diff --git a/flybrains/templates.py b/flybrains/templates.py
@@ -28,6 +28,7 @@
 __all__ = ['FCWB', 'IBN', 'IBNWB', 'IS2', 'JFRC2', 'T1', 'Dmel', 'DsecI',
            'Dsim', 'Dvir', 'JFRC2013', 'JFRC2013DS', 'JRC2018F', 'JRC2018U',
            'JRCFIB2018F', 'JRCFIB2018Fraw', 'JRCFIB2018Fum', 'JRCVNC2018F',
+           'JRCFIB2022M',
            'JRCVNC2018M',
            'JRCVNC2018U',
            'VNCIS1',
@@ -66,14 +67,19 @@ def __repr__(self):
         return self.__str__()
 
     def __str__(self):
+        units = getattr(self, 'units', 'units NA')
+
+        if isinstance(units, list):
+            units = units[0]
+
         if getattr(self, 'boundingbox'):
             bbox = f"""\
-            Bounding box ({self.units[0] if getattr(self, 'units') else 'NA'}):
+            Bounding box ({units}):
               x = {self.boundingbox[0]}, y = {self.boundingbox[2]}, z = {self.boundingbox[4]},
               x = {self.boundingbox[1]}, y = {self.boundingbox[3]}, z = {self.boundingbox[5]},"""
         else:
             bbox = f"""\
-            Bounding box ({self.units[0] if getattr(self, 'units') else 'units NA'}):
+            Bounding box ({units}):
               NA"""
 
         if getattr(self, 'dims'):
@@ -546,7 +552,7 @@ class _JRC2018U(FlyTemplateBrain):
 
 
 class _JRCFIB2018F(FlyTemplateBrain):
-    """JRCFIB2018F aka hemibrain dataset.
+    """JRCFIB2018F aka "hemibrain" dataset.
 
     The JRCFIB2018F reference brain is a stitched FIB SEM volume completed at
     HHMI Janelia Research Campus in 2018.
@@ -658,6 +664,23 @@ def bbox(self):
 
 JRCFIB2018Fraw = _JRCFIB2018Fraw(**template_meta['JRCFIB2018Fraw'])
 
+class _JRCFIB2022M(FlyTemplateBrain):
+    """JRCFIB2022M aka "male CNS" dataset.
+
+    The JRCFIB2022M EM volume is a whole male CNS (brain + VNC) currently being
+    generated by FlyEM at HHMI Janelia Research Campus. At this point, only the
+    brain portion of the volume is available.
+
+    The mesh was generated from a point cloud of automaticaly detected synaptic
+    t-bars.
+
+    The JRCFIB2022Mraw reference brain is uncalibrated (i.e. has units of raw
+    pixels), whereas JRCFIB2022M and JRCFIB2022Mum have units of nanometers
+    and microns with 8x8x8nm isotropic voxels, respectively.
+
+    """
+
+JRCFIB2022M = _JRCFIB2022M(**template_meta['JRCFIB2022M'])
 
 class _JRCVNC2018F(FlyTemplateBrain):
     """JRC2018 reference ventral nerve chords.
@@ -963,6 +986,7 @@ def register_templates():
                  JRCFIB2018Fraw, JRCVNC2018F, JRCVNC2018U, JRCVNC2018M, VNCIS1,
                  FAFB14, FAFB,
                  FLYWIRE,
+                 JRCFIB2022M,
                  FANC, DmelL1CNS_Seymour, COURT2017VNS, COURT2018VNS]
 
     for tmp in templates: