Validation status of Data Readers
WhiteEtAl1986
Data from White et al. 1986, The Structure of the Nervous System of the Nematode Caenorhabditis elegans, Phil. Trans. R. Soc. Lond. B3141–340 (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 1987 thesis. 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 been copied into our repository here.
However, an updated version of this file was used in the DurbinDataReader in cect, as the following minor issues were found in the file, and these were incorporated in the data source, as opposed to the Python reader, for clarity:
Issue 1) Line 2 in the original file (ADAL ADAR Gap_junction 1) was missing JSH or N2U, and so assuming N2U as "ADAL ADAR Gap_junction JSH 2" was already present. Issue 2) While most gap junction connections contained both A->B and B->A connections, but some were missing the reverse connection. The missing connections at the top of the 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.
The "White Whole" dataset is effectively the same as the Varshney et al. 2011 dataset, apart from also containing the connections to/from the pharynx. This dataset was obtained from the WormNeuroAtlas source code, 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 DurbinJSHDataReader
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 2026-07-07 with cect v0.3.2
Validation tests for DurbinN2UDataReader
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 2026-07-07 with cect v0.3.2
Validation tests for White_whole
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
Note: only cells/connections in ConnectomeView: NonpharyngealH included (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
Note: only cells/connections in ConnectomeView: NonpharyngealH included (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 2026-07-07 with cect v0.3.2
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 post cells and added to the connection test yaml file.
Validation tests for VarshneyDataReader
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
Note: only cells/connections in ConnectomeView: NonpharyngealH included (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
Note: only cells/connections in ConnectomeView: NonpharyngealH included (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 2026-07-07 with cect v0.3.2
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 ("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 Bentley2016MAReader
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 2026-07-07 with cect v0.3.2
Validation tests for Bentley2016PepReader
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 2026-07-07 with cect v0.3.2
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 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.
Additionally, we used g1P, not g1p for the name of this pharyngeal glial 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 Cook2019HermReader
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 2026-07-07 with cect v0.3.2
Validation tests for Cook2019MaleReader
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 2026-07-07 with cect v0.3.2
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 was 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 have been included and some of these tested below also.
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 appended to 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 Cook2020DataReader
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 2026-07-07 with cect v0.3.2
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 BrittinDataReader
Contact connections
| Pre | Post | Expected weight | Match |
|---|---|---|---|
| ADAL | ADLL | 11319.5 | Yes |
| ADLL | ADAL | 11319.5 | Yes |
| ADLR | ADAR | 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 2026-07-07 with cect v0.3.2
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.
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 WitvlietDataReader1
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 2026-07-07 with cect v0.3.2
Validation tests for WitvlietDataReader2
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 2026-07-07 with cect v0.3.2
Validation tests for WitvlietDataReader3
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 2026-07-07 with cect v0.3.2
Validation tests for WitvlietDataReader4
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 2026-07-07 with cect v0.3.2
Validation tests for WitvlietDataReader5
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 2026-07-07 with cect v0.3.2
Validation tests for WitvlietDataReader6
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 2026-07-07 with cect v0.3.2
Validation tests for WitvlietDataReader7
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 2026-07-07 with cect v0.3.2
Validation tests for WitvlietDataReader8
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 2026-07-07 with cect v0.3.2
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 (the false discovery rate, i.e. the probability that a neuron pair declared "functionally connected" is actually a false positive). We used a q_max = 0.05 and just added that to the adjacency matrix used in this example.
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 WormNeuroAtlasFuncReader
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 2026-07-07 with cect v0.3.2
RipollSanchezEtAl2023
Data on neuropeptidergic signalling 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-, medium- 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 (numbers of matched peptides expressed in pre cell with corresponding receptor in post cell) read off, to provide checks listed below.
Validation tests for RipollSanchezShortRangeReader
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 2026-07-07 with cect v0.3.2
Validation tests for RipollSanchezMidRangeReader
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 2026-07-07 with cect v0.3.2
Validation tests for RipollSanchezLongRangeReader
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 2026-07-07 with cect v0.3.2
YimEtAl2024
Data on the dauer connectivity was obtained from the supplementary information of: Yim et al. 2024, Comparative connectomics of dauer reveals developmental plasticity Nature Communications, 15:1546.
Supplementary Data 3 links to file 41467_2024_45943_MOESM6_ESM.xlsx.
This file has been added to our repository here.
Contactome based/non-normalised data
The spreadsheet above contained a sheet named "Dauer", from where the values for the contact area of connections were read. This file was opened in Excel and weights of selected connections were visually read from the cells, noting the pre and post cells and added to the connection test yaml file.
Normalised data
The spreadsheet above contained a sheet named "Dauer_normalized", from where the values for the "normalized" connections were read. This file was opened in Excel and weights of selected connections were visually read from the cells, noting the pre and post cells and added to the connection test yaml file.
Validation tests for Yim2024NonNormDataReader
Contact 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 2026-07-07 with cect v0.3.2
Validation tests for Yim2024DataReader
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 2026-07-07 with cect v0.3.2
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 2015.
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 towards known connected anatomical (or monoaminergic) postsynaptic targets of these.
Validation tests for Wang2024HermReader
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 2026-07-07 with cect v0.3.2
Validation tests for Wang2024MaleReader
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: 3889 (matches)
Expected total weight of connections: 3889 (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: 1722 (matches)
Expected total weight of connections: 1722 (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: 691 (matches)
Expected total weight of connections: 691 (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 2026-07-07 with cect v0.3.2