add MANC dataset:

- template (incl. mesh) for MANC and MANCraw
- JRC2018M <-> MANC transform download

flybrains/data/template_meta.json

@@ -1006,7 +1006,7 @@
          "nanometers"
       ],
       "_navis_units": "1 nanometer",
-      "description": "The Female Adult Nerve Cord electron microscopy dataset (nicknamed FANC, pronounced “fancy”) was generated by Jasper Phelps with help from other members of Wei-Chung Lee’s lab. See Phelps et al., Cell (2021) for details.",
+      "description": "The Female Adult Nerve Cord electron microscopy dataset (nicknamed FANC, pronounced “fancy”) was generated by Jasper Phelps with help from other members of the Wei-Chung Lee lab. See Phelps et al., Cell (2021) for details.",
       "doi": "10.1016/j.cell.2020.12.013",
       "boundingbox": [
          0,
@@ -1053,5 +1053,41 @@
          6050,
          248100
       ]
+   },
+   {
+      "name": "Male Adult Nerve Cord",
+      "type": null,
+      "sex": "male",
+      "voxdims": [
+         8,
+         8,
+         8
+      ],
+      "origin": [
+         0.0,
+         0.0,
+         0.0
+      ],
+      "boundingbox": [
+         6148,
+         42844,
+         5123,
+         50859,
+         2026,
+         64819
+      ],
+      "units": [
+         "voxels",
+         "voxels",
+         "voxels"
+      ],
+      "description": "Janelia Male Adult Nerve Cord (MANC) EM dataset.",
+      "label": "MANC",
+      "dims": [
+         36696,
+         45736,
+         62793
+      ],
+      "doi": "10.1101/2023.06.05.543757"
    }
 ]

flybrains/download.py

@@ -304,6 +304,7 @@ def download_jrc_vnc_transforms(data_home=None, skip_existing=True):
     Includes:
       - JRCVNC2018U <-> JRCVNC2018F (110Mb)
       - JRCVNC2018U <-> JRCVNC2018M (150Mb)
+      - JRCVNC2018M <-> MANC (1Gb)
 
     Parameters
     ----------
@@ -319,13 +320,15 @@ def download_jrc_vnc_transforms(data_home=None, skip_existing=True):
     data_home = get_data_home(data_home, create=True)
     urls = (
         "28909212?private_link=c4589cef9180e1dd4ee1",
-        "28908795?private_link=42ad71eb14e7dd51e81a")
+        "28908795?private_link=42ad71eb14e7dd51e81a",
+        "38827794")
     urls = [f"https://ndownloader.figshare.com/files/{f}" for f in urls]
 
     # Note that we are renaming the files upon download!
     filenames = (
         'JRCVNC2018U_JRCVNC2018F.h5',  # originally: JRC2018VncU_JRC2018VncF.h5
         'JRCVNC2018M_JRCVNC2018U.h5',  # originally: JRC2018VncM_JRC2018VncU.h5
+        'JRCVNC2018M_MANC.h5',  # originally: JRC2018VncM_MANC.h5
       )
 
     print(f'Downloading JRC (Saalfeld lab) VNC transforms into {data_home}')

flybrains/templates.py

@@ -37,7 +37,9 @@
            'VNCIS1',
            'FAFB14', 'FAFB',
            'FLYWIRE',
-           'FANC', 'DmelL1CNS_Seymour',
+           'FANC',
+           "MANC", "MANCraw",
+           'DmelL1CNS_Seymour',
            'COURT2017VNS', 'COURT2018VNS',
            'register_templates']
 
@@ -1005,11 +1007,13 @@ class _FANC(FlyTemplateBrain):
     """Female Adult Nerve Cord
 
     Using a serial-section electron microscopy (EM) to acquire a synapse-resolution
-    dataset containing the ventral nerve cord (VNC) of an adult female Drosophila melanogaster.
+    dataset containing the ventral nerve cord (VNC) of an adult female Drosophila
+    melanogaster.
 
     References
     ----------
-    Reconstruction of motor control circuits in adult Drosophila using automated transmission electron microscopy
+    Reconstruction of motor control circuits in adult Drosophila using automated
+    transmission electron microscopy
     Jasper S Phelps, David Grant Colburn Hildebrand, Brett J Graham, Aaron T Kuan,
     Logan A Thomas, Tri M Nguyen, Julia Buhmann, Anthony W Azevedo, Anne Sustar,
     Sweta Agrawal, Mingguan Liu, Brendan L Shanny, Jan Funke, John C Tuthill,
@@ -1021,6 +1025,66 @@ class _FANC(FlyTemplateBrain):
 FANC = _FANC(**template_meta['FANC'])
 
 
+class _MANC(FlyTemplateBrain):
+    """Male Adult Nerve Cord.
+
+    A FIBSEM volume containing a ventral nerve cord of an adult male
+    Drosophila melanogaster.
+
+    References
+    ----------
+    A Connectome of the Male Drosophila Ventral Nerve Cord
+    Shin-ya Takemura, Kenneth J Hayworth, Gary B Huang, Michal Januszewski,
+    Zhiyuan Lu, Elizabeth C Marin, Stephan Preibisch, C Shan Xu, John Bogovic,
+    Andrew S Champion, Han SJ Cheong, Marta Costa, Katharina Eichler,
+    William Katz, Christopher Knecht, Feng Li, Billy J Morris, Christopher Ordish,
+    Patricia K Rivlin, Philipp Schlegel, Kazunori Shinomiya, Tomke Stürner,
+    Ting Zhao, Griffin Badalamente, Dennis Bailey, Paul Brooks, Brandon S Canino,
+    Jody Clements, Michael Cook, Octave Duclos, Christopher R Dunne, Kelli Fairbanks,
+    Siqi Fang, Samantha Finley-May, Audrey Francis, Reed George, Marina Gkantia,
+    Kyle Harrington, Gary Patrick Hopkins, Joseph Hsu, Philip M Hubbard,
+    Alexandre Javier, Dagmar Kainmueller, Wyatt Korff, Julie Kovalyak,
+    Dominik Krzemiński, Shirley A Lauchie, Alanna Lohff, Charli Maldonado,
+    Emily A Manley, Caroline Mooney, Erika Neace, Matthew Nichols, Omotara Ogundeyi,
+    Nneoma Okeoma, Tyler Paterson, Elliott Phillips, Emily M Phillips,
+    Caitlin Ribeiro, Sean M Ryan, Jon Thomson Rymer, Anne K Scott, Ashley L Scott,
+    David Shepherd, Aya Shinomiya, Claire Smith, Natalie Smith, Alia Suleiman,
+    Satoko Takemura, Iris Talebi, Imaan FM Tamimi, Eric T Trautman, Lowell Umayam,
+    John J Walsh, Tansy Yang, Gerald M Rubin, Louis K Scheffer, Jan Funke,
+    Stephan Saalfeld, Harald F Hess, Stephen M Plaza, Gwyneth M Card,
+    Gregory SXE Jefferis, Stuart Berg
+    bioRxiv 2023.06.05.543757; doi: https://doi.org/10.1101/2023.06.05.543757
+
+    """
+    @property
+    def mesh(self):
+        """On-demand loading of surface mesh."""
+        if not hasattr(self, '_mesh'):
+            # Load the raw mesh (voxels)
+            fp = os.path.join(mesh_filepath, f'{self.label}raw.ply')
+            self._mesh = tm.load_mesh(fp)
+            # Convert voxels to nanometers
+            if self.units[0] == 'nm':
+                self._mesh.vertices *= 8
+        return self._mesh
+
+
+# MANC in nanometers
+MANC = _MANC(**template_meta['MANC'])
+MANC.boundingbox = [b * 8 for b in MANC.boundingbox]
+MANC.dims = [b * 8 for b in MANC.dims]
+MANC.units = ['nm', 'nm', 'nm']
+
+
+class _MANCraw(FlyTemplateBrain):
+    """Male Adult Nerve Cord."""
+
+
+# MANC in raw voxels (original)
+MANCraw = _MANCraw(**template_meta['MANC'])
+MANCraw.label = 'MANCraw'
+
+
 class _DmelL1CNS_Seymour(FlyTemplateBrain):
     """L1 CNS ssTEM at 3.8x3.8x50 nm of whole Drosophila 1st instar larval CNS.
 
@@ -1046,7 +1110,9 @@ def register_templates():
                  FAFB14, FAFB, FLYWIRE,
                  JRCFIB2022M,JRCFIB2022Mraw,
                  JRCFIB2018F, JRCFIB2018Fraw,
-                 FANC, DmelL1CNS_Seymour, COURT2017VNS, COURT2018VNS]
+                 FANC, MANC, MANCraw,
+                 DmelL1CNS_Seymour,
+                 COURT2017VNS, COURT2018VNS]
 
     for tmp in templates:
         transforms.registry.register_templatebrain(tmp, skip_existing=True)