Validation status of C. elegans Connectome Toolbox Data Readers
These tests aim to ensure the connectivity data accessed through the Connectome Toolbox API matches the data present in the original publications. Each Dataset is associated with a specific publication, and each of these contains one or more DataReaders for the different types of connectome data it contains (e.g. for hermaphrodite and male worms).
The entries below for each of the Datasets currently incorporated into the C. elegans Connectome Toolbox include:
- A brief description of the original publication from which the data is taken.
- Information on the supplementary data file(s) etc. from which the connectivity data were extracted.
- A list of any issues found with these data files, and what steps were taken to address these issues.
- Links to the final version of the (updated) files which have been included in the Connectome Toolbox repository (generally stored here).
The source files (e.g. Excel spreadsheets) containing the original data were manually opened/inspected and values for specific quantities extracted (e.g. specific weight of connection between cell A and cell B, total numbers of connections found).
For each individual DataReader associated with a publication there will be:
- A description of focus/scope of that DataReader (e.g., a specific developmental stage or sex).
- A link to a YAML file containing the expected data for that reader (e.g. manually extracted values from source Excel spreadsheets), which is used to validate the data.
- A set of tables, one for each of the synapse types included in the data (e.g. chemical and electrical), comparing the expected data with the actual data extracted from running the equivalent call in the Connectome Toolbox API.
The full suite of tests is run automatically as part of the continuous integration (CI) tests for the Connectome Toolbox on GitHub, and any mismatches between the expected and actual data will cause the CI tests to fail. Successfully passing the tests on the main branch of the repository will deploy the latest version of the website, which includes the most up-to-date validation summary.
WhiteEtAl1986
Data from White et al. 1986, The Structure of the Nervous System of the Nematode Caenorhabditis elegans, Phil. Trans. R. Soc. Lond. B 314 (1165): 1–340 (also on WormAtlas).
As described on WormAtlas, the primary structured dataset describing this connectivity is the neurodata.txt file which was compiled by Richard Durbin in his thesis (Studies on the Development and Organisation of the Nervous System of Caenorhabditis elegans. University of Cambridge; 1987). This (and the Readme describing it) can be found on WormAtlas.
The neurodata.txt file describes reconstructed connectivity for 2 animals: an N2U (adult hermaphrodite) and JSH (which Durbin described as an L4 male; it is now believed that this animal was an L4 hermaphrodite). This file has been copied into our repository here.
We noted however a small number of minor issues (described below) that were found in the original data file. These updates were incorporated in cect by using an updated version of this file (neurodata_updated.txt, in our repository here), as opposed to being fixed in the source of our Python reader (DurbinDataReader), for clarity. The issues are:
Issue 1) Line 2 in the original file (ADAL ADAR Gap_junction 1) did not specify the animal (JSH or N2U). As an equivalent JSH entry (ADAL ADAR Gap_junction JSH 2) was already present, we assumed line 2 referred to N2U.
Issue 2) While most gap junction connections contained both A->B and B->A connections, some were missing the reverse connection. The missing connections have been included at the top of the updated file.
Issue 3) One gap junction connection had a different weight for the A->B and B->A connections (RIML<->AVAR). Updated the weight to be the same for both directions, using the larger of the two weights.
This file is the source of two of our readers below, DurbinJSHDataReader and DurbinN2UDataReader. A third, White_whole, is effectively the same as the Varshney et al. 2011 dataset (VarshneyDataReader), apart from also containing the connections to/from the pharynx. See the VarshneyDataReader description for how that dataset builds on the JSH and N2U data.
This White_whole dataset was obtained from a file in the WormNeuroAtlas source code (here), and copied to our repository here.
Note: this dataset contained 3 electrical connections not present in the Varshney dataset: PLML <-> BDUL, PLMR <-> BDUR, RID <-> RID, all of weight 1.
Validation tests for DataReader: DurbinJSHDataReader
DataReader Description: Chemical and electrical connectivity of the JSH L4 worm from White et al. 1986 data, based on the neurodata.txt file from R. M. Durbin's thesis, 1987. See validation information for minor changes from that file.
Source YAML file with expected values. The tests below compare this list of expected values of a small number of connection weights, along with total numbers of connections in the source data files, with the actual values extracted from the Connectome Toolbox API.
Chemical synaptic connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| ADAL | AVBR | 5 | Yes |
| ADFR | AIZR | 10 | Yes |
| DVC | RIGL | 8 | Yes |
| RMDDR | RMDVL | 10 | Yes |
Expected number of nonzero connection weights: 1350 (matches).
Expected total weight of connections: 4000 (matches).
Electrical connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| AVAL | AVAR | 2 | Yes |
| RMED | IL1VL | 2 | Yes |
| CEPDL | OLQDL | 4 | Yes |
| AVAL | SABD | 2 | Yes |
| SABD | AVAL | 2 | Yes |
Electrical synapse. Symmetric connectivity matrix: True
Expected number of nonzero connection weights: 586 (matches).
Expected total weight of connections: 1546 (matches).
Validation PASSED on 2026-09-29 with cect v0.3.5
Validation tests for DataReader: DurbinN2UDataReader
DataReader Description: Chemical and electrical connectivity of the N2U (adult hermaphrodite) worm from White et al. 1986 data, based on the neurodata.txt file from R. M. Durbin's thesis, 1987. See validation information for minor changes from that file.
Source YAML file with expected values. The tests below compare this list of expected values of a small number of connection weights, along with total numbers of connections in the source data files, with the actual values extracted from the Connectome Toolbox API.
Chemical synaptic connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| ADAL | AVBR | 7 | Yes |
| ADFR | AIZR | 8 | Yes |
| DVC | RIGL | 5 | Yes |
| RMDDR | RMDVL | 12 | Yes |
Expected number of nonzero connection weights: 1486 (matches).
Expected total weight of connections: 4056 (matches).
Electrical connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| AVAL | AVAR | 1 | Yes |
| RMED | IL1VL | 1 | Yes |
| CEPDL | OLQDL | 1 | Yes |
| VA2 | PLNR | 1 | Yes |
| PLNR | VA2 | 1 | Yes |
| DVC | VD1 | 2 | Yes |
| VD1 | DVC | 2 | Yes |
Electrical synapse. Symmetric connectivity matrix: True
Expected number of nonzero connection weights: 556 (matches).
Expected total weight of connections: 692 (matches).
Validation PASSED on 2026-09-29 with cect v0.3.5
Validation tests for DataReader: White_whole
DataReader Description: Reanalysis of the White et al. 1986 connectome data by Varshney et al. 2011. This version includes the pharynx.
Source YAML file with expected values. The tests below compare this list of expected values of a small number of connection weights, along with total numbers of connections in the source data files, with the actual values extracted from the Connectome Toolbox API.
Chemical synaptic connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| AVAL | AS5 | 3 | Yes |
| ADAL | AVBR | 7 | Yes |
| ADFR | AIZR | 8 | Yes |
| DVC | RIGL | 5 | Yes |
| RMDDR | RMDVL | 12 | Yes |
| VD3 | BWM | 23 | Yes |
| URADR | BWM | 7 | Yes |
| IL1DL | BWM | 5 | Yes |
Expected number of nonzero connection weights: 2386 (matches).
Expected total weight of connections: 7943 (matches).
Expected number of cells: 309 (matches).
Chemical connections (view: NonpharyngealH)
Note: these tests only apply to a "view" of the White_whole data, specifically only cells/connections in ConnectomeView: NonpharyngealH are included. The description of this view is: All hermaphrodite neurons except those in the pharynx.
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| AVAL | AS5 | 3 | Yes |
| ADAL | AVBR | 7 | Yes |
| ADFR | AIZR | 8 | Yes |
| DVC | RIGL | 5 | Yes |
| RMDDR | RMDVL | 12 | Yes |
Expected number of nonzero connection weights: 2194 (matches).
Expected total weight of connections: 6394 (matches).
Electrical connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| AVAL | AVAR | 5 | Yes |
| RMED | IL1VL | 1 | Yes |
| CEPDL | OLQDL | 1 | Yes |
| PDER | PDEL | 3 | Yes |
Electrical synapse. Symmetric connectivity matrix: True
Expected number of nonzero connection weights: 1144 (matches).
Expected total weight of connections: 1928 (matches).
Electrical connections (view: NonpharyngealH)
Note: these tests only apply to a "view" of the White_whole data, specifically only cells/connections in ConnectomeView: NonpharyngealH are included. The description of this view is: All hermaphrodite neurons except those in the pharynx.
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| AVAL | AVAR | 5 | Yes |
| RMED | IL1VL | 1 | Yes |
| CEPDL | OLQDL | 1 | Yes |
| PDER | PDEL | 3 | Yes |
Expected number of nonzero connection weights: 1036 (matches).
Expected total weight of connections: 1782 (matches).
Validation PASSED on 2026-09-29 with cect v0.3.5
VarshneyEtAl2011
An updated version of the White et al. 1986 wiring data, as presented in Varshney et al. 2011, Structural Properties of the Caenorhabditis elegans Neuronal Network. PLOS Computational Biology 7(2): e1001066.
The file NeuronConnect.xls, referenced in the paper ("The collected data is available from the WormAtlas"), which is also available here, has been copied into our repository here, and used in our DataReader.
The spreadsheet above contained a single sheet, with a list of presynaptic cells, postsynaptic cells, synapse numbers, and types of synapse (S, Sp, R, Rp, EJ, NMJ). See here for full details. This file was opened in Excel and weights of selected connections were visually read from the cells (summing entries for S and Sp where both were present), noting the pre- and postsynaptic cells and added to the connection test YAML file.
Validation tests for DataReader: VarshneyDataReader
DataReader Description: A corrected and extended version of the White et al. 1986 chemical and electrical wiring diagram, incorporating original Mind of a Worm data, Durbin's unpublished reconstructions, new EM imaging of previously unimaged dorsal cord regions, and over 3,000 synapse additions or corrections, particularly in the ventral cord motorneuron connectivity. Excludes pharyngeal neurons, but includes neuromuscular junction connections, all to one BWM (body wall muscle cell).
Source YAML file with expected values. The tests below compare this list of expected values of a small number of connection weights, along with total numbers of connections in the source data files, with the actual values extracted from the Connectome Toolbox API.
Chemical synaptic connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| AVAL | AS5 | 3 | Yes |
| ADAL | AVBR | 7 | Yes |
| ADFR | AIZR | 8 | Yes |
| DVC | RIGL | 5 | Yes |
| RMDDR | RMDVL | 12 | Yes |
| VD3 | BWM | 23 | Yes |
| URADR | BWM | 7 | Yes |
| IL1DL | BWM | 5 | Yes |
Expected number of nonzero connection weights: 2309 (matches).
Expected total weight of connections: 7804 (matches).
Chemical connections (view: NonpharyngealH)
Note: these tests only apply to a "view" of the VarshneyDataReader data, specifically only cells/connections in ConnectomeView: NonpharyngealH are included. The description of this view is: All hermaphrodite neurons except those in the pharynx.
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| AVAL | AS5 | 3 | Yes |
| ADAL | AVBR | 7 | Yes |
| ADFR | AIZR | 8 | Yes |
| DVC | RIGL | 5 | Yes |
| RMDDR | RMDVL | 12 | Yes |
Expected number of nonzero connection weights: 2194 (matches).
Expected total weight of connections: 6394 (matches).
Electrical connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| AVAL | AVAR | 5 | Yes |
| RMED | IL1VL | 1 | Yes |
| CEPDL | OLQDL | 1 | Yes |
| PDER | PDEL | 3 | Yes |
Electrical synapse. Symmetric connectivity matrix: True
Expected number of nonzero connection weights: 1031 (matches).
Expected total weight of connections: 1777 (matches).
Electrical connections (view: NonpharyngealH)
Note: these tests only apply to a "view" of the VarshneyDataReader data, specifically only cells/connections in ConnectomeView: NonpharyngealH are included. The description of this view is: All hermaphrodite neurons except those in the pharynx.
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| AVAL | AVAR | 5 | Yes |
| RMED | IL1VL | 1 | Yes |
| CEPDL | OLQDL | 1 | Yes |
| PDER | PDEL | 3 | Yes |
Expected number of nonzero connection weights: 1031 (matches).
Expected total weight of connections: 1777 (matches).
Validation PASSED on 2026-09-29 with cect v0.3.5
BentleyEtAl2016
Data from: The Multilayer Connectome of Caenorhabditis elegans, Bentley et al. 2016, PLoS Comput Biol 12(12): e1005283
Connectivity was originally released in supplementary information: S1 Dataset, a zip file ("Included are edge lists for monoamine and neuropeptide networks").
The contents of this zip file were extracted and the 2 files edge_lists/edgelist_MA.csv and edge_lists/edgelist_NP.csv were added to our repository and used in the monoaminergic and peptidergic DataReaders respectively.
For the validation tests below, specific connections between pre and postsynaptic cells were read out from the edgelist_MA.csv and edgelist_NP.csv files above and a weight of 1 was added to the connection test YAML file for these.
Validation tests for DataReader: Bentley2016MAReader
DataReader Description: Data on monoaminergic connectivity from Bentley et al. 2016 (i.e. dopaminergic, tyraminergic, octopaminergic & serotonergic extrasynaptic transmission).
Source YAML file with expected values. The tests below compare this list of expected values of a small number of connection weights, along with total numbers of connections in the source data files, with the actual values extracted from the Connectome Toolbox API.
Dopamine connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| CEPDR | ALNR | 1 | Yes |
| ADER | VA11 | 1 | Yes |
| PDEL | SIBDR | 1 | Yes |
| ADEL | CANL | 1 | Yes |
| CEPDR | CANL | 1 | Yes |
Expected number of nonzero connection weights: 1176 (matches).
Tyramine connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| RIML | IL1DL | 1 | Yes |
| RIML | PVT | 1 | Yes |
| RIMR | AFDL | 1 | Yes |
| RIML | CANL | 1 | Yes |
Expected number of nonzero connection weights: 228 (matches).
Octopamine connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| RICL | PHAL | 1 | Yes |
| RICL | ADEL | 1 | Yes |
| RICR | SIAVL | 1 | Yes |
Expected number of nonzero connection weights: 56 (matches).
Serotonin connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| ADFR | M2R | 1 | Yes |
| NSMR | AIBL | 1 | Yes |
| HSNL | M3L | 1 | Yes |
Expected number of nonzero connection weights: 492 (matches).
Validation PASSED on 2026-09-29 with cect v0.3.5
Validation tests for DataReader: Bentley2016PepReader
DataReader Description: Data on peptidergic connectivity from Bentley et al. 2016 (i.e. extrasynaptic transmission via neuropeptides).
Source YAML file with expected values. The tests below compare this list of expected values of a small number of connection weights, along with total numbers of connections in the source data files, with the actual values extracted from the Connectome Toolbox API.
Peptidergic connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| AIAL | AIAR | 1 | Yes |
| RMER | OLQVR | 1 | Yes |
| M3R | RIVR | 1 | Yes |
| FLPR | IL2R | 1 | Yes |
| VD9 | PVWR | 1 | Yes |
Expected number of nonzero connection weights: 7078 (matches).
Validation PASSED on 2026-09-29 with cect v0.3.5
CookEtAl2019
Data was taken from: Cook et al. 2019, Whole-animal connectomes of both Caenorhabditis elegans sexes. Nature 571, 63–71.
Three spreadsheets with these connections have been identified:
1) Original Supplementary information 5
Connectivity matrices were released in the following supplementary information file with the publication: 41586_2019_1352_MOESM9_ESM.xlsx.
Note: there is a slight internal consistency issue in this file - some of the male ray structural cells are named R1stL, R2stR, etc., but in other locations the names R1shL, R2shR, etc. are used.
2) WormWiring original adjacency matrices
On WormWiring (Emmons lab), there is a link: Original Connectome Adjacency Matrices (ref 1, SI5) SI 5 Connectome adjacency matrices.xlsx.
Note: there is a slight difference between this file and the original - some of the male ray structural cells R1stL, R2stR cells have been changed to R1shL, R2shR, etc. in this file.
3) WormWiring corrected adjacency matrices
There is also a file: Hermaphrodite and Male Connectomes (Adjacency Matrices), Adults (corrected July 2020) [SI 5 Connectome adjacency matrices, corrected July 2020.xlsx].
The differences in this file are as follows:
Hermaphrodite gap junctions
- Added: PVDL ↔ hmc: weight 400
- Added: PVDR ↔ hmc: weight 400
- Removed: BDUR ↔ PLMR: weight 23
- The following connections were not originally present in both directions (i.e. a fully symmetrical electrical connection was not present):
- DD06 ↔ PDB
- ALA ↔ exc_gl
- VA09 ↔ PVCR
Male gap junctions
- Added: DD1 ↔ MVL08: weight 2
- Removed: RIVR ↔ FLPL: weight 1
- The following connections were not originally present in both directions (i.e. a fully symmetrical electrical connection was not present):
- DD1 ↔ MVR08
- R8AL ↔ R8BL
- RIVL ↔ FLPL
- VB6 ↔ VB7
- VB7 ↔ VB5
- MDR08 ↔ DD1
In Connectome Toolbox, we use spreadsheet 3), and use R1stL, R2stR, etc., as these are the names used on WormAtlas.
In Cook et al. 2019, Supplementary Information 4, g1P, g1AL, g1AR, g2L & g2R were listed under "glial cell". We have used "pharyngeal gland cell" for their types, as this is what is used in Cook et al. 2020.
Additionally, we used g1P, not g1p for the name of this pharyngeal gland cell, as this is the form used in Cook et al. 2020, as well as on WormWiring.
This file was opened in Excel and weights of selected connections were visually read from the cells on the specific sheets (e.g. "hermaphrodite chemical", "male gap jn symmetric"), noting the pre and post cells and these added to the connection test YAML file, along with the total number of nonzero connections in each adjacency matrix as well as the total weights.
Validation tests for DataReader: Cook2019HermReader
DataReader Description: Chemical and electrical connectivity of the hermaphrodite from Cook et al. 2019, including connections between neurons, muscles and other cells.
Source YAML file with expected values. The tests below compare this list of expected values of a small number of connection weights, along with total numbers of connections in the source data files, with the actual values extracted from the Connectome Toolbox API.
Chemical synaptic connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| I1R | I2R | 6 | Yes |
| SMBDL | SDQR | 18 | Yes |
| VC2 | PVT | 6 | Yes |
| DB4 | MDL13 | 4 | Yes |
| RIMR | MDL05 | 15 | Yes |
| M1 | g1P | 5 | Yes |
| I6 | g1P | 2 | Yes |
Expected number of nonzero connection weights: 4879 (matches).
Expected total weight of connections: 28113 (matches).
Electrical connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| M4 | pm5VL | 1 | Yes |
| g1AL | M4 | 7 | Yes |
| PLNL | PHCL | 2 | Yes |
| PVDL | ALA | 250 | Yes |
| PVDL | hmc | 400 | Yes |
| PVDR | hmc | 400 | Yes |
| DD6 | PDB | 2 | Yes |
| PDB | DD6 | 2 | Yes |
| ALA | exc_gl | 1 | Yes |
| exc_gl | ALA | 1 | Yes |
| BDUL | PLML | 0 | Yes |
| RMDVR | SMDVR | 8 | Yes |
Electrical synapse. Symmetric connectivity matrix: True
Expected number of nonzero connection weights: 2883 (matches).
Expected total weight of connections: 23313 (matches).
Validation PASSED on 2026-09-29 with cect v0.3.5
Validation tests for DataReader: Cook2019MaleReader
DataReader Description: Chemical and electrical connectivity of the male from Cook et al. 2019, including connections between neurons, muscles and other cells.
Source YAML file with expected values. The tests below compare this list of expected values of a small number of connection weights, along with total numbers of connections in the source data files, with the actual values extracted from the Connectome Toolbox API.
Chemical synaptic connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| I1R | I2R | 6 | Yes |
| SMBDL | SDQR | 18 | Yes |
| R7BL | PDC | 34 | Yes |
| DB4 | MDL13 | 4 | Yes |
| RIMR | MDL05 | 15 | Yes |
| CEPDR | RMHL | 6 | Yes |
| URBL | OLLL | 4 | Yes |
| R9BR | R7stR | 2 | Yes |
Expected number of nonzero connection weights: 5306 (matches).
Expected total weight of connections: 45959 (matches).
Electrical connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| M4 | pm5VL | 1 | Yes |
| g1AL | M4 | 7 | Yes |
| CANL | exc_cell | 200 | Yes |
| PVDL | ALA | 250 | Yes |
| URBL | IL2L | 17 | Yes |
| DD1 | MVL08 | 2 | Yes |
| RIVR | FLPL | 0 | Yes |
| DD1 | MVR08 | 2 | Yes |
| R8AL | R8BL | 5 | Yes |
| RIVL | FLPL | 1 | Yes |
| VB6 | VB7 | 5 | Yes |
| VB7 | VB5 | 1 | Yes |
| MDR08 | DD1 | 2 | Yes |
Electrical synapse. Symmetric connectivity matrix: True
Expected number of nonzero connection weights: 3482 (matches).
Expected total weight of connections: 31702 (matches).
Validation PASSED on 2026-09-29 with cect v0.3.5
CookEtAl2020
Data was taken from Cook et al. 2020, The connectome of the Caenorhabditis elegans pharynx, J Comp Neurol. 2020; 528: 2767–2784.
The connectivity data were released in 2 CSV files in the supplementary information for that paper:
-
cne24932-sup-0004-Supinfo4.csv described as "Complete edge list for pharyngeal reconstruction."
-
cne24932-sup-0005-Supinfo5.csv described as "Inferred gap junction connectivity between end-organs". These connections are included and some of these are tested below.
These files were opened in Apple Numbers, and the weights (numbers of connections between pairs of cells, electrical or chemical) were read off, to provide checks listed below.
Validation issue: Repeated connections
There were multiple entries in cne24932-sup-0004-Supinfo4.csv for the same pair of cells and the same type of connection. Where there are multiple lines of this type, the weights in the new line have been added to (summed with) the existing weight.
This is a summary of the connections which were repeated:
Existing connection at (14,14) (M4->M4, Chemical), was: 15.0, new conn weight: 15.0, appended weight is: 30.000000
Existing connection at (17,30) (I4->NSMR, Chemical), was: 2.0, new conn weight: 13.5, appended weight is: 15.500000
Existing connection at (37,15) (NSML->pm5D, Chemical), was: 29.0, new conn weight: 9.0, appended weight is: 38.000000
Existing connection at (30,31) (NSMR->bm, Chemical), was: 50.0, new conn weight: 11.0, appended weight is: 61.000000
Existing connection at (30,15) (NSMR->pm5D, Chemical), was: 1.0, new conn weight: 8.5, appended weight is: 9.500000
Existing connection at (30,32) (NSMR->M3R, Chemical), was: 15.0, new conn weight: 7.5, appended weight is: 22.500000
Existing connection at (37,18) (NSML->pm5VL, Chemical), was: 58.0, new conn weight: 5.0, appended weight is: 63.000000
Existing connection at (17,18) (I4->pm5VL, Chemical), was: 6.0, new conn weight: 4.5, appended weight is: 10.500000
Existing connection at (37,31) (NSML->bm, Chemical), was: 78.0, new conn weight: 5.0, appended weight is: 83.000000
Existing connection at (17,34) (I4->M2L, Chemical), was: 1.0, new conn weight: 4.0, appended weight is: 5.000000
Existing connection at (32,8) (M3R->g1AR, Chemical), was: 1.0, new conn weight: 1.5, appended weight is: 2.500000
Existing connection at (6,14) (I5->M4, Chemical), was: 8.0, new conn weight: 18.5, appended weight is: 26.500000
Existing connection at (6,30) (I5->NSMR, Chemical), was: 3.0, new conn weight: 17.5, appended weight is: 20.500000
Existing connection at (37,16) (NSML->pm5VR, Chemical), was: 3.0, new conn weight: 7.0, appended weight is: 10.000000
Existing connection at (37,38) (NSML->M3L, Chemical), was: 14.0, new conn weight: 6.5, appended weight is: 20.500000
Existing connection at (6,16) (I5->pm5VR, Chemical), was: 8.0, new conn weight: 3.5, appended weight is: 11.500000
Existing connection at (25,41) (I1R->I2R, Chemical), was: 5.0, new conn weight: 3.0, appended weight is: 8.000000
Existing connection at (9,15) (M1->pm5D, Chemical), was: 3.0, new conn weight: 1.0, appended weight is: 4.000000
Existing connection at (6,8) (I5->g1AR, Chemical), was: 4.0, new conn weight: 1.0, appended weight is: 5.000000
Existing connection at (6,7) (I5->g1AL, Chemical), was: 7.0, new conn weight: 1.0, appended weight is: 8.000000
Existing connection at (33,27) (I1L->I2L, Chemical), was: 10.0, new conn weight: 1.0, appended weight is: 11.000000
Existing connection at (14,6) (M4->I5, Chemical), was: 1.0, new conn weight: 0.5, appended weight is: 1.500000
Existing connection at (36,14) (I6->M4, Chemical), was: 3.0, new conn weight: 9.5, appended weight is: 12.500000
Existing connection at (36,37) (I6->NSML, Chemical), was: 13.0, new conn weight: 8.0, appended weight is: 21.000000
Existing connection at (35,16) (M2R->pm5VR, Chemical), was: 9.0, new conn weight: 3.0, appended weight is: 12.000000
Existing connection at (34,7) (M2L->g1AL, Chemical), was: 2.0, new conn weight: 3.0, appended weight is: 5.000000
Existing connection at (42,43) (MCL->mc2V, Chemical), was: 10.0, new conn weight: 2.5, appended weight is: 12.500000
Existing connection at (9,23) (M1->I3, Chemical), was: 6.0, new conn weight: 1.0, appended weight is: 7.000000
Existing connection at (9,27) (M1->I2L, Chemical), was: 2.0, new conn weight: 1.0, appended weight is: 3.000000
Existing connection at (25,9) (I1R->M1, Chemical), was: 2.0, new conn weight: 1.0, appended weight is: 3.000000
Existing connection at (25,23) (I1R->I3, Chemical), was: 5.0, new conn weight: 1.0, appended weight is: 6.000000
Existing connection at (32,14) (M3R->M4, Chemical), was: 1.0, new conn weight: 1.0, appended weight is: 2.000000
Existing connection at (36,30) (I6->NSMR, Chemical), was: 3.0, new conn weight: 1.0, appended weight is: 4.000000
Existing connection at (36,15) (I6->pm5D, Chemical), was: 14.0, new conn weight: 1.0, appended weight is: 15.000000
Existing connection at (14,17) (M4->I4, Chemical), was: 4.0, new conn weight: 0.5, appended weight is: 4.500000
Existing connection at (9,19) (M1->g1P, Chemical), was: 4.0, new conn weight: 0.5, appended weight is: 4.500000
Existing connection at (0,0) (M5->M5, GapJunction), was: 1.0, new conn weight: 1.0, appended weight is: 2.000000
Existing connection at (14,14) (M4->M4, GapJunction), was: 1.0, new conn weight: 1.0, appended weight is: 2.000000
Existing connection at (60,49) (mc1DR->pm4VR, GapJunction), was: 3.0, new conn weight: 3.0, appended weight is: 6.000000
Existing connection at (49,60) (pm4VR->mc1DR, GapJunction), was: 3.0, new conn weight: 3.0, appended weight is: 6.000000
Validation tests for DataReader: Cook2020DataReader
DataReader Description: Chemical and electrical connectivity of the C. elegans pharynx, from Cook et al 2020, including connections between pharyngeal neurons, muscles and other cells (epithelial, gland and marginal).
Source YAML file with expected values. The tests below compare this list of expected values of a small number of connection weights, along with total numbers of connections in the source data files, with the actual values extracted from the Connectome Toolbox API.
Chemical synaptic connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| I1R | I2R | 8 | Yes |
| I1R | I2L | 1 | Yes |
| RIPL | pm3VL | 4 | Yes |
| I5 | g1AR | 5 | Yes |
| I5 | g1AL | 8 | Yes |
| I6 | g1P | 2 | Yes |
Expected number of nonzero connection weights: 259 (matches).
Electrical connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| M4 | pm5VL | 1 | Yes |
| e2DR | e3D | 2 | Yes |
| g1AL | M3L | 2 | Yes |
| pm1 | pm2VL | 3 | Yes |
| mc1V | pm3VL | 3 | Yes |
| mc3V | pm7VL | 3 | Yes |
| mc3DR | pm8 | 3 | Yes |
Electrical synapse. Symmetric connectivity matrix: True
Expected number of nonzero connection weights: 246 (matches).
Validation PASSED on 2026-09-29 with cect v0.3.5
Brittin2021
Data taken from: A multi-scale brain map derived from whole-brain volumetric reconstructions, Christopher A. Brittin, Steven J. Cook, David H. Hall, Scott W. Emmons & Netta Cohen, Nature 591, 105–110, 2021.
Supplementary data file 3 (41586_2021_3284_MOESM5_ESM.xlsx) containing the Mδ, Cδ and Gδ reference graphs was downloaded and used in the BrittinDataReader.
The M4 graph is the example used in Connectome Toolbox. Values for the contact area/weights in tab M, with delta = 4 were used for this, and the values below were read from the spreadsheet.
Validation tests for DataReader: BrittinDataReader
DataReader Description: Contactome information from Brittin et al. 2021. This dataset contains the contact area between pairs of cells in the C. elegans nerve ring, as measured from volumetric reconstructions of the JSH and N2U animals, based on the previously published electron micrographs from White et al. 1986. The M4 graph as described in the Brittin et al. 2021 paper is used here (i.e. limited to contacts that are conserved across the left and right sides of the JSH and N2U animals).
Source YAML file with expected values. The tests below compare this list of expected values of a small number of connection weights, along with total numbers of connections in the source data files, with the actual values extracted from the Connectome Toolbox API.
Contact connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| ADAL | ADLL | 11319.5 | Yes |
| ADLL | ADAL | 11319.5 | Yes |
| ADLR | ADAR | 11319.5 | Yes |
| ADAR | ADLR | 11319.5 | Yes |
| RID | RICL | 10043.5 | Yes |
| RICL | RID | 10043.5 | Yes |
| RICR | RID | 10043.5 | Yes |
| RIAR | SIBVR | 5114.25 | Yes |
| AQR | RIAL | 2010.75 | Yes |
| AQR | RIAR | 2010.75 | Yes |
| RIAR | AQR | 2010.75 | Yes |
| RIAL | AQR | 2010.75 | Yes |
Expected number of nonzero connection weights: 3850 (matches).
Validation PASSED on 2026-09-29 with cect v0.3.5
WitvlietEtAl2021
Data on neuronal connectivity at different developmental stages of C. elegans from: Connectomes across development reveal principles of brain maturation Witvliet et al. Nature 2021 596:257–261.
While the paper's supplementary information contained connectivity matrices (here), these only contain the chemical connections.
The 8 spreadsheet files (witvliet_2020_1 L1.xlsx, witvliet_2020_2 L1.xlsx, ..., witvliet_2020_8 adult.xlsx) hosted on WormWiring also contain electrical connectivity, and are saved to our repository here, and used for the readers.
The chemical connection weights below were read from the supplementary information spreadsheet, and the electrical connection weights were taken from the WormWiring spreadsheet.
Validation tests for DataReader: WitvlietDataReader1
DataReader Description: Chemical and electrical connectivity from Witvliet et al. 2021, dataset 1 (L1 stage)
Source YAML file with expected values. The tests below compare this list of expected values of a small number of connection weights, along with total numbers of connections in the source data files, with the actual values extracted from the Connectome Toolbox API.
Chemical synaptic connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| AWAL | AWBL | 2 | Yes |
| AINR | AUAL | 2 | Yes |
| RIAL | RMDVR | 6 | Yes |
Expected number of nonzero connection weights: 775 (matches).
Electrical connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| ASHL | ADAL | 9 | Yes |
| RMDR | SMDVR | 1 | Yes |
| IL1R | IL1VR | 2 | Yes |
Electrical synapse. Symmetric connectivity matrix: True
Expected number of nonzero connection weights: 164 (matches).
Validation PASSED on 2026-09-29 with cect v0.3.5
Validation tests for DataReader: WitvlietDataReader2
DataReader Description: Chemical and electrical connectivity from Witvliet et al. 2021, dataset 2 (L1 stage)
Source YAML file with expected values. The tests below compare this list of expected values of a small number of connection weights, along with total numbers of connections in the source data files, with the actual values extracted from the Connectome Toolbox API.
Chemical synaptic connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| ADLR | ASKR | 4 | Yes |
| AUAL | RIBL | 3 | Yes |
| AWBL | AIZL | 2 | Yes |
Expected number of nonzero connection weights: 986 (matches).
Electrical connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| AVJR | RIS | 1 | Yes |
| OLLL | OLLR | 2 | Yes |
| RIH | RIR | 1 | Yes |
Electrical synapse. Symmetric connectivity matrix: True
Expected number of nonzero connection weights: 246 (matches).
Validation PASSED on 2026-09-29 with cect v0.3.5
Validation tests for DataReader: WitvlietDataReader3
DataReader Description: Chemical and electrical connectivity from Witvliet et al. 2021, dataset 3 (L1 stage)
Source YAML file with expected values. The tests below compare this list of expected values of a small number of connection weights, along with total numbers of connections in the source data files, with the actual values extracted from the Connectome Toolbox API.
Chemical synaptic connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| ADLR | ASKR | 4 | Yes |
| FLPR | FLPL | 3 | Yes |
| RIVL | GLRVR | 2 | Yes |
Expected number of nonzero connection weights: 1012 (matches).
Electrical connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| OLLR | RIGR | 1 | Yes |
| OLLL | OLLR | 2 | Yes |
| SMDDL | SMDDR | 1 | Yes |
Electrical synapse. Symmetric connectivity matrix: True
Expected number of nonzero connection weights: 186 (matches).
Validation PASSED on 2026-09-29 with cect v0.3.5
Validation tests for DataReader: WitvlietDataReader4
DataReader Description: Chemical and electrical connectivity from Witvliet et al. 2021, dataset 4 (L1 stage)
Source YAML file with expected values. The tests below compare this list of expected values of a small number of connection weights, along with total numbers of connections in the source data files, with the actual values extracted from the Connectome Toolbox API.
Chemical synaptic connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| AWCR | AWCL | 5 | Yes |
| RIML | MDR04 | 2 | Yes |
| RIVL | MVR07 | 1 | Yes |
Expected number of nonzero connection weights: 1136 (matches).
Electrical connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| ALML | AVDR | 2 | Yes |
| AVER | URYVL | 1 | Yes |
| SMDDL | SMDDR | 1 | Yes |
Electrical synapse. Symmetric connectivity matrix: True
Expected number of nonzero connection weights: 415 (matches).
Validation PASSED on 2026-09-29 with cect v0.3.5
Validation tests for DataReader: WitvlietDataReader5
DataReader Description: Chemical and electrical connectivity from Witvliet et al. 2021, dataset 5 (L2 stage)
Source YAML file with expected values. The tests below compare this list of expected values of a small number of connection weights, along with total numbers of connections in the source data files, with the actual values extracted from the Connectome Toolbox API.
Chemical synaptic connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| ADLR | ASHR | 3 | Yes |
| ALNR | SAAVR | 2 | Yes |
| BAGR | RIBL | 13 | Yes |
Expected number of nonzero connection weights: 1515 (matches).
Electrical connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| ADAR | ASHR | 2 | Yes |
| ADLL | CEPshVL | 1 | Yes |
| OLQVL | RIGL | 2 | Yes |
Electrical synapse. Symmetric connectivity matrix: True
Expected number of nonzero connection weights: 578 (matches).
Validation PASSED on 2026-09-29 with cect v0.3.5
Validation tests for DataReader: WitvlietDataReader6
DataReader Description: Chemical and electrical connectivity from Witvliet et al. 2021, dataset 6 (L3 stage)
Source YAML file with expected values. The tests below compare this list of expected values of a small number of connection weights, along with total numbers of connections in the source data files, with the actual values extracted from the Connectome Toolbox API.
Chemical synaptic connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| ASER | ASEL | 1 | Yes |
| ASKR | AIAR | 18 | Yes |
| ALML | CEPVL | 3 | Yes |
Expected number of nonzero connection weights: 1525 (matches).
Electrical connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| AIZR | AWCL | 2 | Yes |
| BAGR | RIR | 1 | Yes |
| DVA | OLQVL | 1 | Yes |
Electrical synapse. Symmetric connectivity matrix: True
Expected number of nonzero connection weights: 426 (matches).
Validation PASSED on 2026-09-29 with cect v0.3.5
Validation tests for DataReader: WitvlietDataReader7
DataReader Description: Chemical and electrical connectivity from Witvliet et al. 2021, dataset 7 (adult stage)
Source YAML file with expected values. The tests below compare this list of expected values of a small number of connection weights, along with total numbers of connections in the source data files, with the actual values extracted from the Connectome Toolbox API.
Chemical synaptic connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| AQR | BAGR | 4 | Yes |
| ALNR | SAAVR | 11 | Yes |
| CEPDL | OLLL | 7 | Yes |
Expected number of nonzero connection weights: 2202 (matches).
Electrical connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| ADAL | PVQL | 2 | Yes |
| SIAVL | SMDVR | 1 | Yes |
| SAADL | SMBDL | 2 | Yes |
Electrical synapse. Symmetric connectivity matrix: True
Expected number of nonzero connection weights: 576 (matches).
Validation PASSED on 2026-09-29 with cect v0.3.5
Validation tests for DataReader: WitvlietDataReader8
DataReader Description: Chemical and electrical connectivity from Witvliet et al. 2021, dataset 8 (adult stage)
Source YAML file with expected values. The tests below compare this list of expected values of a small number of connection weights, along with total numbers of connections in the source data files, with the actual values extracted from the Connectome Toolbox API.
Chemical synaptic connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| ASER | AWCR | 9 | Yes |
| ALNL | SAAVL | 10 | Yes |
| ALML | BDUL | 9 | Yes |
Expected number of nonzero connection weights: 2186 (matches).
Electrical connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| ADFL | AIAL | 3 | Yes |
| AFDR | AIZR | 1 | Yes |
| PVT | RIBL | 2 | Yes |
Electrical synapse. Symmetric connectivity matrix: True
Expected number of nonzero connection weights: 612 (matches).
Validation PASSED on 2026-09-29 with cect v0.3.5
RandiEtAl2023
Functional connectivity data of C. elegans from: Randi et al. 2023, Neural signal propagation atlas of Caenorhabditis elegans, Nature 623, 406–414 (2023).
We used the WormNeuroAtlas package as discussed in the paper to provide the signal propagation map values. The method get_signal_propagation_map() specifying the wildtype data (strain="wt") was used to get the post-stimulus calcium response amplitude (⟨ΔF/F₀⟩ₜ) matrix, while get_signal_propagation_q() was used to get the q-values (i.e. the minimum false discovery rate at which that pair would be called significant). Only pairs with q < max_q = 0.05 were included in the adjacency matrix for the example we use.
We obtained the validation values below by calling the above functions and printing the value in the signal propagation for specific connections, checking q < 0.05.
Validation tests for DataReader: WormNeuroAtlasFuncReader
DataReader Description: Data on functional connectivity of C. elegans from WormNeuroAtlas Python package (values extracted with get_signal_propagation_map() & get_signal_propagation_q(), with max_q (q being the false discovery rate) = 0.05)
Source YAML file with expected values. The tests below compare this list of expected values of a small number of connection weights, along with total numbers of connections in the source data files, with the actual values extracted from the Connectome Toolbox API.
Functional connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| ASER | ASHL | 0 | Yes |
| I1L | MI | -0.12525142862743782 | Yes |
| MCR | M2R | 1.1917423178652604 | Yes |
| AVBR | AVEL | -0.14791430582009063 | Yes |
| AVEL | AVEL | 0 | Yes |
Expected number of nonzero connection weights: 1150 (matches).
Validation PASSED on 2026-09-29 with cect v0.3.5
RipollSanchezEtAl2023
Data on neuropeptidergic signaling has been taken from: Ripoll-Sánchez et al. 2023, The neuropeptidergic connectome of C. elegans. Neuron, Volume 111, Issue 22, 2023, Pages 3570-3589.e5.
There is a GitHub repository referenced in the paper: https://github.com/LidiaRipollSanchez/Neuropeptide-Connectome. There are 3 different models used for the neuropeptidergic connectome (short-, mid- and long-range), and the following files have been used in Connectome Toolbox as the source of these models:
- 01022024_neuropeptide_connectome_short_range_model.csv
- 01022024_neuropeptide_connectome_mid_range_model.csv
- 01022024_neuropeptide_connectome_long_range_model.csv
For each of these CSV files, the file was opened in Apple Numbers, and the weights (number of different NPP-GPCR pathways) read off, to provide checks listed below.
Validation tests for DataReader: RipollSanchezShortRangeReader
DataReader Description: Dataset of neuropeptidergic connections only between neurons whose processes overlap in the same neuronal process bundle
Source YAML file with expected values. The tests below compare this list of expected values of a small number of connection weights, along with total numbers of connections in the source data files, with the actual values extracted from the Connectome Toolbox API.
Peptidergic connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| I3 | I5 | 3 | Yes |
| URBL | RMDDL | 4 | Yes |
| RIVR | HSNL | 6 | Yes |
Expected number of nonzero connection weights: 31417 (matches).
Validation PASSED on 2026-09-29 with cect v0.3.5
Validation tests for DataReader: RipollSanchezMidRangeReader
DataReader Description: Dataset of neuropeptidergic connections between any neurons whose processes lie within the same broad body region (head, midbody, or tail)
Source YAML file with expected values. The tests below compare this list of expected values of a small number of connection weights, along with total numbers of connections in the source data files, with the actual values extracted from the Connectome Toolbox API.
Peptidergic connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| PVR | I3 | 6 | Yes |
| SABVL | VC1 | 1 | Yes |
| RIR | AVKR | 5 | Yes |
Expected number of nonzero connection weights: 40425 (matches).
Validation PASSED on 2026-09-29 with cect v0.3.5
Validation tests for DataReader: RipollSanchezLongRangeReader
DataReader Description: Dataset of neuropeptidergic connections between any neuron pair regardless of anatomical location
Source YAML file with expected values. The tests below compare this list of expected values of a small number of connection weights, along with total numbers of connections in the source data files, with the actual values extracted from the Connectome Toolbox API.
Peptidergic connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| I3 | I5 | 3 | Yes |
| URBL | RMDDL | 4 | Yes |
| RIVR | HSNL | 6 | Yes |
| PVR | I3 | 6 | Yes |
| SABVL | VC1 | 1 | Yes |
| RIR | AVKR | 5 | Yes |
| VC4 | I4 | 1 | Yes |
| ALA | HSNR | 11 | Yes |
Expected number of nonzero connection weights: 53558 (matches).
Validation PASSED on 2026-09-29 with cect v0.3.5
YimEtAl2024
Data on the dauer connectivity, comprising both directed synaptic connections and contact area matrices, was obtained from the supplementary information of: Nature Communications, 15:1546.
Two distinct types of connection information are used from this paper:
A) Synaptic connectivity (Supplementary Data 3). A directed matrix, with rows presynaptic and columns postsynaptic. Presynaptic active zones were detected by a convolutional neural network, reconstructed in 3D and proofread; postsynaptic partners and each partner's share of an active zone were assigned by simulating neurotransmitter diffusion. Weights are the summed volume (nm³) of active zone material attributed to a pre/post pair.
B) Contact area (Supplementary Data 6). A symmetric matrix, as physical apposition has no pre/post polarity, measured from the volumetric segmentation rather than from synapses. Weights are the summed area (nm²) of contact between two cells.
Both are available as raw values and normalized by the standard deviation of weights excluding the top 5% of weights, the latter easing comparison with other datasets.
Supplementary Data 3 in the paper links to file 41467_2024_45943_MOESM6_ESM.xlsx. This file has been added to our repository here.
Supplementary Data 6 in the paper links to file 41467_2024_45943_MOESM9_ESM.xlsx. This file has been added to our repository here.
Both of the Supplementary Data 3 & 6 spreadsheets contained sheets named "Dauer" and "Dauer_normalized", from where the values for the non normalized and normalized, respectively, synaptic weights/contact areas of connections were read.
Each file was opened in Excel and weights of selected connections were visually read from the spreadsheet cells, noting the pre and post cells, and the values were added to the connection test YAML file for validation below.
Validation tests for DataReader: Yim2024NonNormDataReader
DataReader Description: Reconstruction of the directed chemical synaptic connectome of the dauer, a distinct developmental stage of C. elegans. Presynaptic active zones were detected by a convolutional neural network, reconstructed in 3D and proofread; postsynaptic partners and each partner's share of an active zone were assigned by simulating neurotransmitter diffusion.
Source YAML file with expected values. The tests below compare this list of expected values of a small number of connection weights, along with total numbers of connections in the source data files, with the actual values extracted from the Connectome Toolbox API.
Chemical synaptic connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| RIH | CEPshDL | 7464.984227 | Yes |
| PVNL | ALMR | 97686.4 | Yes |
| URYDR | URADR | 33663.09403 | Yes |
Expected number of nonzero connection weights: 2198 (matches).
Validation PASSED on 2026-09-29 with cect v0.3.5
Validation tests for DataReader: Yim2024DataReader
DataReader Description: Reconstruction of the directed chemical synaptic connectome of the dauer, a distinct developmental stage of C. elegans. Presynaptic active zones were detected by a convolutional neural network, reconstructed in 3D and proofread; postsynaptic partners and each partner's share of an active zone were assigned by simulating neurotransmitter diffusion. This connectome dataset contains normalized weights to ease comparison to other datasets.
Source YAML file with expected values. The tests below compare this list of expected values of a small number of connection weights, along with total numbers of connections in the source data files, with the actual values extracted from the Connectome Toolbox API.
Chemical synaptic connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| ADFR | AFDR | 0.428024049927915 | Yes |
| SMBDL | RMED | 6.01978135910464 | Yes |
| ASHL | RIPL | 1.20804164634321 | Yes |
Expected number of nonzero connection weights: 2198 (matches).
Validation PASSED on 2026-09-29 with cect v0.3.5
Validation tests for DataReader: Yim2024ContactomeNonNormDataReader
DataReader Description: Reconstruction of the contactome of the dauer, a distinct developmental stage of C. elegans, contains a symmetric matrix measuring physical contact between pairs of cells. Every cell in the reconstructed EM volume was traced voxel by voxel; these labeled cells were then expanded until the extracellular gaps between them closed, and the area of each resulting point of contact summed.
Source YAML file with expected values. The tests below compare this list of expected values of a small number of connection weights, along with total numbers of connections in the source data files, with the actual values extracted from the Connectome Toolbox API.
Contact connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| ADFR | AFDR | 1527984 | Yes |
| AFDR | ADFR | 1527984 | Yes |
| RIH | CEPshDL | 251712 | Yes |
| PVNL | ALMR | 290064 | Yes |
| URYDR | URADR | 537136 | Yes |
Expected number of nonzero connection weights: 12160 (matches).
Validation PASSED on 2026-09-29 with cect v0.3.5
Validation tests for DataReader: Yim2024ContactomeDataReader
DataReader Description: Reconstruction of the contactome of the dauer, a distinct developmental stage of C. elegans, contains a symmetric matrix measuring physical contact between pairs of cells. Every cell in the reconstructed EM volume was traced voxel by voxel; these labeled cells were then expanded until the extracellular gaps between them closed, and the area of each resulting point of contact summed. This connectome dataset contains normalized contact areas/weights to ease comparison to other datasets.
Source YAML file with expected values. The tests below compare this list of expected values of a small number of connection weights, along with total numbers of connections in the source data files, with the actual values extracted from the Connectome Toolbox API.
Contact connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| ADFR | AFDR | 3.47775177807871 | Yes |
| SMBDL | RMED | 1.7182985712879 | Yes |
| ASHL | RIPL | 1.92777331045848 | Yes |
| RIPL | ASHL | 1.92777331045848 | Yes |
Expected number of nonzero connection weights: 12160 (matches).
Validation PASSED on 2026-09-29 with cect v0.3.5
WangEtAl2024
This reader combines neurotransmitter expression values from: Wang et al. 2024 (A neurotransmitter atlas of C. elegans males and hermaphrodites, eLife 13:RP95402) with basic anatomical connectivity information from Cook et al. 2019, and monoaminergic receptor expression information from Bentley et al. 2016.
Supplementary file 2 in that publication contains the expression patterns of neurotransmitter pathway genes in hermaphrodites.
This has been added to our repository here.
Supplementary file 3 contains the expression patterns of neurotransmitter pathway genes in male-specific neurons.
This has been added to our repository here.
These files were used to identify potential presynaptic cells for each neurotransmitter, and then validation tests were added for known anatomically (or monoaminergically) connected postsynaptic targets of these.
Note: while Cook et al. 2019 contains hermaphrodite and male specific anatomical connectomes, the data from Bentley et al. 2016 is hermaphrodite only, and is used for both sexes here.
Validation tests for DataReader: Wang2024HermReader
DataReader Description: This dataset for the hermaphrodite C. elegans contains neurotransmitter expression values from: Wang et al. 2024 with basic anatomical connectivity information from Cook et al. 2019, and monoaminergic receptor expression information from Bentley et al. 2016
Source YAML file with expected values. The tests below compare this list of expected values of a small number of connection weights, along with total numbers of connections in the source data files, with the actual values extracted from the Connectome Toolbox API.
Acetylcholine connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| I1R | I2R | 1 | Yes |
| SMBDL | SDQR | 1 | Yes |
| VC2 | PVT | 1 | Yes |
| DB4 | MDL13 | 1 | Yes |
| M1 | g1P | 1 | Yes |
Expected number of nonzero connection weights: 2756 (matches).
Expected total weight of connections: 2756 (matches).
Glutamate connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| RIMR | MDL05 | 1 | Yes |
| PHBR | AVAR | 1 | Yes |
| URYDL | OLQDL | 1 | Yes |
| PVR | IL1DR | 1 | Yes |
Expected number of nonzero connection weights: 1334 (matches).
Expected total weight of connections: 1334 (matches).
Betaine connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| ASIL | AIBL | 1 | Yes |
| NSMR | pm5VR | 1 | Yes |
| RIR | AQR | 1 | Yes |
Expected number of nonzero connection weights: 150 (matches).
Expected total weight of connections: 150 (matches).
GABA connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| RIBL | CEPVL | 1 | Yes |
| VD10 | MVR20 | 1 | Yes |
| SMDDL | SIBDL | 1 | Yes |
Expected number of nonzero connection weights: 506 (matches).
Expected total weight of connections: 506 (matches).
Dopamine connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| CEPVL | AIMR | 1 | Yes |
| PDEL | RICR | 1 | Yes |
| ADEL | DD4 | 1 | Yes |
Expected number of nonzero connection weights: 1176 (matches).
Expected total weight of connections: 1176 (matches).
Serotonin connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| HSNL | PVQL | 1 | Yes |
| NSML | VD3 | 1 | Yes |
| ADFR | RID | 1 | Yes |
Expected number of nonzero connection weights: 492 (matches).
Expected total weight of connections: 492 (matches).
Tyramine connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| RIMR | RMEV | 1 | Yes |
| RIMR | SIADL | 1 | Yes |
| RIML | VD5 | 1 | Yes |
Expected number of nonzero connection weights: 228 (matches).
Expected total weight of connections: 228 (matches).
Octopamine connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| RICR | ASIL | 1 | Yes |
| RICL | SIAVR | 1 | Yes |
| RICL | PVQL | 1 | Yes |
Expected number of nonzero connection weights: 56 (matches).
Expected total weight of connections: 56 (matches).
Validation PASSED on 2026-09-29 with cect v0.3.5
Validation tests for DataReader: Wang2024MaleReader
DataReader Description: This dataset for the male C. elegans contains neurotransmitter expression values from: Wang et al. 2024 with basic anatomical connectivity information from Cook et al. 2019, and monoaminergic receptor expression information from Bentley et al. 2016
Source YAML file with expected values. The tests below compare this list of expected values of a small number of connection weights, along with total numbers of connections in the source data files, with the actual values extracted from the Connectome Toolbox API.
Acetylcholine connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| I1R | I2R | 1 | Yes |
| SMBDL | SDQR | 1 | Yes |
| DB4 | MDL13 | 1 | Yes |
| M1 | g1P | 1 | Yes |
Expected number of nonzero connection weights: 3155 (matches).
Expected total weight of connections: 3155 (matches).
Glutamate connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| RIMR | MDL05 | 1 | Yes |
| CP05 | AVG | 1 | Yes |
| R9AL | HOB | 1 | Yes |
Expected number of nonzero connection weights: 1368 (matches).
Expected total weight of connections: 1368 (matches).
Betaine connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| ASIL | AIBL | 1 | Yes |
| NSMR | pm5VR | 1 | Yes |
| RIR | AQR | 0 | Yes |
| RIR | DVA | 1 | Yes |
Expected number of nonzero connection weights: 96 (matches).
Expected total weight of connections: 96 (matches).
GABA connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| RIBL | CEPVL | 0 | Yes |
| RIBL | RIS | 1 | Yes |
| VD10 | MVR20 | 0 | Yes |
| VD10 | MVL20 | 1 | Yes |
| SMDDL | SIBDL | 1 | Yes |
Expected number of nonzero connection weights: 606 (matches).
Expected total weight of connections: 606 (matches).
Dopamine connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| CEPVL | AIMR | 1 | Yes |
| PDEL | RICR | 1 | Yes |
| ADEL | DD4 | 1 | Yes |
Expected number of nonzero connection weights: 1160 (matches).
Expected total weight of connections: 1160 (matches).
Serotonin connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| NSML | VD3 | 1 | Yes |
| ADFR | RID | 1 | Yes |
Expected number of nonzero connection weights: 328 (matches).
Expected total weight of connections: 328 (matches).
Tyramine connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| RIMR | RMEV | 1 | Yes |
| RIMR | SIADL | 1 | Yes |
| RIML | VD5 | 1 | Yes |
Expected number of nonzero connection weights: 224 (matches).
Expected total weight of connections: 224 (matches).
Octopamine connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| RICR | ASIL | 1 | Yes |
| RICL | SIAVR | 1 | Yes |
| RICL | PVQL | 1 | Yes |
Expected number of nonzero connection weights: 56 (matches).
Expected total weight of connections: 56 (matches).
Validation PASSED on 2026-09-29 with cect v0.3.5