Age determination of Atlantic cod (Gadus morhua): 2012 Workshop between Canada and France on cod otoliths. Final report of the project SALMOCODAGE
Bibliographic record
Abstract
France and Canada have been working closely together for numerous years under the governance of The Northwest Atlantic Fisheries Organisation (NAFO) that regulates fisheries in the Northwest Atlantic. This workshop was the first step to achieve greater agreement in the estimation of age from calcified pieces between the scientific experts from those 2 countries. The goal of this project is to realize a calibration of the estimation of ages from cod (Gadus morhua) between France and Canada in order to optimize the precision of the data supplied by those countries for stock assessment purposes. There has been in the past an internal workshop for Atlantic Canada in 1997 on ageing fish and numerous workshops for Northeast Atlantic, more precisely for the Baltic and North sea under the governance of the International Council for the Exploration of the Sea (ICES). This workshop has been organized in St-Pierre et Miquelon from 10 to 14 September 2012 and regrouped 6 scientists from IFREMER (France) and the Department of Fisheries and Oceans (DFO). This meeting was subsidized by the Ministry of Overseas (France) and the Territorial Council of St-Pierre et Miquelon. Prior to this workshop a sample of 451 otoliths and otolith images has been interpreted independently by 3 French and 3 Canadian readers. The sample consisted of 2 samples from the 3Ps NAFO area (Research survey and commercial) and 1 sample from the 3Pn, 4RS NAFO area (from various sources). Two different methods were used to age the otoliths, one using images from sliced otoliths (France) and one using broken (or cut) otoliths (Canada). Both methods used transmitted light. Results from the different sets of calcified pieces showed some differences. The set of cod otoliths from research vessel in 3Ps presented the higher percentage agreement (83%). Of the 236 otoliths, 112 were read with 100% agreement (47.5%). Modal age ot hese fish was comprised between 1 and 13 years with the mean at 4 years. The second set with high percent agreement was composed by cod otoliths from commercial vessels of the same area (3Ps) (71.7%). Of the 115 otoliths, 24 were read with 100% percentage agreement (21%). These fish were older than those from the research vessel. The mean modal age was 6 years (range from 4 to 11). The other set of cod otoliths showed a percentage agreement of 69%. This set was composed of fish both commercial and research vessels from the 3Pn, 4RS area. Of the 100 otoliths, only 7 were read with 100% percentage agreement (7%). Difference in precision could be due to the number of readers (8 for set 3 and only 4 for set 1), the composition of the samples (set 1 was composed of fish younger than other sets) and also of the sampling area. During this workshop it has been be noted that there was certainty of bias among readings from the 3 sets of cod otoliths. Moreover, there is certainty of bias between 2 readings from different methods from the same reader (example: readers 1 and 2 of the set from commercial and research vessels coming from the 3Pn, 4RS areas). The position of the first ring was identified as an important source of bias. Some measurements were taken on otolith images with 100% agreement from TNPC software\nin order to determine distances between nucleus and the settling check, and also from the nucleus to the two first growth rings. Distance analysis will provide tools to identify mismatches between readings and/or readers. The second important source of bias was the difference in the edge interpretation during July and August. When Canadian readers identify the edge with small opaque zone (which is not continuous around the edge), then the last translucent ring is considered as growth ring. In contrary, for the French readers, it is not a growth ring. Ages assigned by the Canadian personnel are generally one year greater than those of participants from France for those months. Therefore, in order to reduce those biases, a guideline on reading methods was presented and a database of reference otolith images was started (where 100% agreement was reached).\nThis first Franco-Canadian meeting on age estimation has identified sources of biases and helped to reduce them. It also produced reference documents common to France and Canada for cod in the Northwest Atlantic. However some differences persist, mainly on the otoliths sampled in July and August and this could be part of future studies.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.015 | 0.006 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.004 | 0.002 |
| Science and technology studies | 0.004 | 0.002 |
| Scholarly communication | 0.002 | 0.001 |
| Open science | 0.002 | 0.004 |
| Research integrity | 0.002 | 0.002 |
| Insufficient payload (model declined to judge) | 0.003 | 0.001 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".