History of fly_hemibrain
The changes to the source code of this entry in the repository, newest first, each with the differences it made to the entry's files. They are also listed on GitLab.
[entries] Add the date when each entry was added, and remove icon_hash beff7c9
The dates are those of the commits that first added the entries' files (2020-08-11 for the entries of the initial commit); renamed entries keep the date of their first name. Changed: none
diff --git a/entries/fly_hemibrain/__init__.py b/entries/fly_hemibrain/__init__.py
index 4499fe9..70ce67b 100644
--- a/entries/fly_hemibrain/__init__.py
+++ b/entries/fly_hemibrain/__init__.py
@@ -34,7 +34,7 @@ The network has the following properties:
tags = ['Biological', 'Connectome', 'Weighted', 'Metadata']
url = 'https://www.janelia.org/project-team/flyem/hemibrain'
citation = [('L. K. Scheffer et al., "A connectome and analysis of the adult Drosophila central brain." eLife 9, e57443 (2020)', 'https://doi.org/10.7554/eLife.57443')]
-icon_hash = '5e29c22b78691ca4060bc765'
+date_added = '2022-11-17'
upstream_license = None
upstream_prefix = 'https://storage.googleapis.com/hemibrain/v1.2'
files = [('exported-traced-adjacencies-v1.2.tar.gz', None, 'csv')]
[entries] Prefix the properties in the descriptions with (Node), (Edge) or (Graph) bc3dbbd
The lists of properties at the end of the descriptions marked edge properties with "Edge" but left node properties unmarked, or grouped them in "Nodes: `a`, ...; `b`, ..." items, so the kind of a property was often unclear. Every item now starts with (Node), (Edge) or (Graph), followed by the property names, a colon and the explanation, one item per property or group of properties; qualifications (kinds of nodes, networks) follow the names in parentheses. Properties that were only named got a short explanation, and a few items that named the wrong kind of property were corrected.
diff --git a/entries/fly_hemibrain/__init__.py b/entries/fly_hemibrain/__init__.py
index a198284..4499fe9 100644
--- a/entries/fly_hemibrain/__init__.py
+++ b/entries/fly_hemibrain/__init__.py
@@ -26,11 +26,11 @@ Connections between a pair of neurons are split according to the primary region
The network has the following properties:
-- `bodyId`: the neuron's identifier in the hemibrain data set (neuPrint body ID).
-- `type`: the cell type of the neuron (e.g. `CL141`, `FS4C`); empty if not assigned.
-- `instance`: the neuron's instance name, typically the cell type followed by additional qualifiers and the brain side (e.g. `FS4C(FQ12)_C4_R`).
-- `roi` (edges): the primary brain region in which the synapses of the connection are located (e.g. `SLP(R)`).
-- `weight` (edges): the number of synapses from $i$ to $j$ in that region."""
+- (Node) `bodyId`: the neuron's identifier in the hemibrain data set (neuPrint body ID).
+- (Node) `type`: the cell type of the neuron (e.g. `CL141`, `FS4C`); empty if not assigned.
+- (Node) `instance`: the neuron's instance name, typically the cell type followed by additional qualifiers and the brain side (e.g. `FS4C(FQ12)_C4_R`).
+- (Edge) `roi` (edges): the primary brain region in which the synapses of the connection are located (e.g. `SLP(R)`).
+- (Edge) `weight` (edges): the number of synapses from $i$ to $j$ in that region."""
tags = ['Biological', 'Connectome', 'Weighted', 'Metadata']
url = 'https://www.janelia.org/project-team/flyem/hemibrain'
citation = [('L. K. Scheffer et al., "A connectome and analysis of the adult Drosophila central brain." eLife 9, e57443 (2020)', 'https://doi.org/10.7554/eLife.57443')]
[entries] Remove unneeded code from the entries 2c69f19
Unneeded "global files" statements, unused imports and variables, f-strings without placeholders, duplicate keys in foodweb_little_rock (keeping the order and the values used), and the second definition of get_lines() in twitter_higgs. Nothing changes in the networks or descriptions. Changed: none
diff --git a/entries/fly_hemibrain/__init__.py b/entries/fly_hemibrain/__init__.py
index fb2a91e..a198284 100644
--- a/entries/fly_hemibrain/__init__.py
+++ b/entries/fly_hemibrain/__init__.py
@@ -47,7 +47,6 @@ def fetch_upstream(force=False):
@coerce_props()
@annotate()
def parse(alts=None):
- global files
name = __name__.split(".")[-1]
for fnames, alt, fmt in files:
if alts is not None and alt not in alts:
[entries] Fix parse bugs and improve the metadata of existing entries c996a0e
From a review of the dataset descriptions against the upstream sources and papers, and from user reports: - parse fixes (wrong edge direction or directedness, shifted or misnamed properties, merged node identities, duplicated or missing edges and nodes, wrong types), e.g. arxiv_citation (the HepTh dates were a copy of the HepPh ones; now from the KDD Cup 2003 data), eu_procurements, foursquare_global, hiv_transmission, genetic_multiplex, gnutella (adds the 05 snapshot), roadnet, macaque_neural, python_dependency - descriptions rewritten from the upstream sources, documenting every property - corrected titles, citations and DOIs, licences (ustream_license typo, the data's own terms), tags and ICON ids - url lists for entries with several sources or dataset pages - SocioPatterns entries moved to the site's new data location, with the daily networks of sp_infectious and sp_primary_school - the Michael Fire entries marked as orphans (served from the mirror) - redundant type forcings removed after the graph-tool coercion fixes
diff --git a/entries/fly_hemibrain/__init__.py b/entries/fly_hemibrain/__init__.py
index e002abe..fb2a91e 100644
--- a/entries/fly_hemibrain/__init__.py
+++ b/entries/fly_hemibrain/__init__.py
@@ -20,13 +20,22 @@ from .. import *
import tarfile
title = "Fly hemibrain (2020)"
-description = """A synaptic map of the hemibrain connectome of fruit fly Drosophila melanogaster. Nodes are neurons, and edges are synaptic connections, traced individually from brain image sections using EM reconstruction techniques. Neurons are labeled by their type. Edges are annotated by the connection strength between the neurons.[^icon]
-[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
+description = r"""The connectome of a large part of the central brain (the "hemibrain") of an adult female fruit fly *Drosophila melanogaster*, reconstructed by the FlyEM project at the Janelia Research Campus from focused ion beam scanning electron microscopy (FIB-SEM) images, with automated segmentation followed by extensive manual proofreading. Nodes are neurons, and a directed edge $(i, j)$ indicates chemical synapses from neuron $i$ (presynaptic) to neuron $j$ (postsynaptic) within a given brain region. This is version v1.2 of the data set, as exported from neuPrint, and includes only the "traced" neurons that are not cropped by the boundaries of the imaged volume.
+
+Connections between a pair of neurons are split according to the primary region of interest (ROI, i.e. brain region) where the synapses reside, so that the same pair of neurons may be connected by several parallel edges, one per ROI. Synapses that lie outside any primary ROI are not included.
+
+The network has the following properties:
+
+- `bodyId`: the neuron's identifier in the hemibrain data set (neuPrint body ID).
+- `type`: the cell type of the neuron (e.g. `CL141`, `FS4C`); empty if not assigned.
+- `instance`: the neuron's instance name, typically the cell type followed by additional qualifiers and the brain side (e.g. `FS4C(FQ12)_C4_R`).
+- `roi` (edges): the primary brain region in which the synapses of the connection are located (e.g. `SLP(R)`).
+- `weight` (edges): the number of synapses from $i$ to $j$ in that region."""
tags = ['Biological', 'Connectome', 'Weighted', 'Metadata']
url = 'https://www.janelia.org/project-team/flyem/hemibrain'
-citation = [('C. Shan Xu et al., "A Connectome of the Adult Drosophila Central Brain." Preprint, https://www.biorxiv.org/content/10.1101/2020.01.21.911859v1 (2020)', 'https://doi.org/10.1101/2020.01.21.911859')]
+citation = [('L. K. Scheffer et al., "A connectome and analysis of the adult Drosophila central brain." eLife 9, e57443 (2020)', 'https://doi.org/10.7554/eLife.57443')]
icon_hash = '5e29c22b78691ca4060bc765'
-ustream_license = None
+upstream_license = None
upstream_prefix = 'https://storage.googleapis.com/hemibrain/v1.2'
files = [('exported-traced-adjacencies-v1.2.tar.gz', None, 'csv')]
@@ -60,7 +69,7 @@ def parse(alts=None):
if i == 0:
continue
v = g.add_vertex()
- vals = line.split(",")
+ vals = line.rstrip("\n").split(",")
vid = int(vals[0])
vids[vid] = v
g.vp.bodyId[v] = vid
@@ -75,7 +84,7 @@ def parse(alts=None):
for i, line in enumerate(f):
if i == 0:
continue
- s, t, roi, w = line.split(",")
+ s, t, roi, w = line.rstrip("\n").split(",")
s = vids[int(s)]
t = vids[int(t)]
e = g.add_edge(s, t)
Update copyright information 73a4f0d
diff --git a/entries/fly_hemibrain/__init__.py b/entries/fly_hemibrain/__init__.py
index 0c28722..e002abe 100644
--- a/entries/fly_hemibrain/__init__.py
+++ b/entries/fly_hemibrain/__init__.py
@@ -1,7 +1,7 @@
#! /usr/bin/env python
# -*- coding: utf-8 -*-
#
-# Copyright (C) 2020-2024 Tiago de Paula Peixoto <tiago@skewed.de>
+# Copyright (C) 2020-2026 Tiago de Paula Peixoto <tiago@skewed.de>
#
# This program is free software: you can redistribute it and/or modify it under
# the terms of the GNU Affero General Public License as published by the Free
Update copyright information 3d288ea
diff --git a/entries/fly_hemibrain/__init__.py b/entries/fly_hemibrain/__init__.py
index 6ecb5eb..0c28722 100644
--- a/entries/fly_hemibrain/__init__.py
+++ b/entries/fly_hemibrain/__init__.py
@@ -1,7 +1,7 @@
#! /usr/bin/env python
# -*- coding: utf-8 -*-
#
-# Copyright (C) 2020-2023 Tiago de Paula Peixoto <tiago@skewed.de>
+# Copyright (C) 2020-2024 Tiago de Paula Peixoto <tiago@skewed.de>
#
# This program is free software: you can redistribute it and/or modify it under
# the terms of the GNU Affero General Public License as published by the Free
Update copyright information 8d005ae
diff --git a/entries/fly_hemibrain/__init__.py b/entries/fly_hemibrain/__init__.py
index 7d22844..6ecb5eb 100644
--- a/entries/fly_hemibrain/__init__.py
+++ b/entries/fly_hemibrain/__init__.py
@@ -1,7 +1,7 @@
#! /usr/bin/env python
# -*- coding: utf-8 -*-
#
-# Copyright (C) 2021 Tiago de Paula Peixoto <tiago@skewed.de>
+# Copyright (C) 2020-2023 Tiago de Paula Peixoto <tiago@skewed.de>
#
# This program is free software: you can redistribute it and/or modify it under
# the terms of the GNU Affero General Public License as published by the Free
Add fly_hemibrain 70064bb
diff --git a/entries/fly_hemibrain/__init__.py b/entries/fly_hemibrain/__init__.py
new file mode 100644
index 0000000..7d22844
--- /dev/null
+++ b/entries/fly_hemibrain/__init__.py
@@ -0,0 +1,84 @@
+#! /usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+# Copyright (C) 2021 Tiago de Paula Peixoto <tiago@skewed.de>
+#
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU Affero General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Affero General Public License along
+# with this program. If not, see <http://www.gnu.org/licenses/>.
+
+from .. import *
+import tarfile
+
+title = "Fly hemibrain (2020)"
+description = """A synaptic map of the hemibrain connectome of fruit fly Drosophila melanogaster. Nodes are neurons, and edges are synaptic connections, traced individually from brain image sections using EM reconstruction techniques. Neurons are labeled by their type. Edges are annotated by the connection strength between the neurons.[^icon]
+[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
+tags = ['Biological', 'Connectome', 'Weighted', 'Metadata']
+url = 'https://www.janelia.org/project-team/flyem/hemibrain'
+citation = [('C. Shan Xu et al., "A Connectome of the Adult Drosophila Central Brain." Preprint, https://www.biorxiv.org/content/10.1101/2020.01.21.911859v1 (2020)', 'https://doi.org/10.1101/2020.01.21.911859')]
+icon_hash = '5e29c22b78691ca4060bc765'
+ustream_license = None
+upstream_prefix = 'https://storage.googleapis.com/hemibrain/v1.2'
+files = [('exported-traced-adjacencies-v1.2.tar.gz', None, 'csv')]
+
+def fetch_upstream(force=False):
+ return fetch_upstream_files(__name__.split(".")[-1], upstream_prefix, files,
+ force)
+
+@cache_network()
+@coerce_props()
+@annotate()
+def parse(alts=None):
+ global files
+ name = __name__.split(".")[-1]
+ for fnames, alt, fmt in files:
+ if alts is not None and alt not in alts:
+ continue
+ if isinstance(fnames, str):
+ fnames = [fnames]
+ with ExitStack() as stack:
+ fs = [stack.enter_context(open_upstream_file(name, fn, "rb")) for fn in fnames]
+ with tarfile.open(fileobj=fs[0]) as tf:
+
+ g = Graph()
+ g.vp.bodyId = g.new_vp("int64_t")
+ g.vp["type"] = g.new_vp("string")
+ g.vp.instance = g.new_vp("string")
+ vids = {}
+ with tf.extractfile("exported-traced-adjacencies-v1.2/traced-neurons.csv") as fb:
+ f = io.TextIOWrapper(fb)
+ for i, line in enumerate(f):
+ if i == 0:
+ continue
+ v = g.add_vertex()
+ vals = line.split(",")
+ vid = int(vals[0])
+ vids[vid] = v
+ g.vp.bodyId[v] = vid
+ g.vp["type"][v] = vals[1]
+ g.vp.instance[v] = vals[2]
+
+ g.ep.weight = g.new_ep("int")
+ g.ep.roi = g.new_ep("string")
+
+ with tf.extractfile("exported-traced-adjacencies-v1.2/traced-roi-connections.csv") as fb:
+ f = io.TextIOWrapper(fb)
+ for i, line in enumerate(f):
+ if i == 0:
+ continue
+ s, t, roi, w = line.split(",")
+ s = vids[int(s)]
+ t = vids[int(t)]
+ e = g.add_edge(s, t)
+ g.ep.roi[e] = roi
+ g.ep.weight[e] = int(w)
+ yield alt, g