Model Classes

Class Description

UCSC IFCB Classifier Classes
Class Name Class ID Common Name AphiaID URN Grouping HAB Description Manual Classifier Notes Example Images
Akashiwo 0 Akashiwo sanguinea 232546 urn:lsid:marinespecies.org:taxname:232546 Dinoflagellate Y Monophyletic, marine dinoflagellate large single cells, kidney-shaped when viewed from top or bottom  
Alexandrium_singlet 1 Alexandium sp. 109470 urn:lsid:marinespecies.org:taxname:109470 Dinoflagellate Y
  1. catenella and others
Originally class was broken out for singles, doublets, etc. But now all Alex is in this class, so the singlet is a misnomer http://akashiwo.oceandatacenter.ucsc.edu:8000/image?image=00032&bin=D20161013T081022_IFCB104
Amy_Gony_Protoc 2 Amylax, Gonyaulax or Protoceratium 109428 urn:lsid:marinespecies.org:taxname:109428 Dinoflagellate Y Descision was made not to distinguish between these, originally with the RF. “Feet” and points visible.  
Asterionellopsis 3 Asterionellopsis 149138 urn:lsid:marinespecies.org:taxname:149138 Diatom N Common species include A. glacialis, A. kariana    
Boreadinium 4 Boredadinium pisiforme 110067 urn:lsid:marinespecies.org:taxname:110067 Dinoflagellate N Slightly compressed thecate cells <45 um  
Centric 5 Centric Diatoms 148965 urn:lsid:marinespecies.org:taxname:148965 Diatom N Order level. Round, or square/rectangle in side view if longer than wide, put in det_cer_lau  
Ceratium 6 Ceratium 109506 urn:lsid:marinespecies.org:taxname:109506 Dinoflagellate N All morphologies Consider splitting up in future  
Chaetoceros 7 Chaetoceros 148985 urn:lsid:marinespecies.org:taxname:148985 Diatom N Single and Chained if setae are forked, Bacteriastrum  
Ciliates 8 Ciliates 11 urn:lsid:marinespecies.org:taxname:11 Cilliate N Small Cilliates ie not belonging to finer scoped classes  
Clusterflagellate 9 Clusteredflagellate 7 urn:lsid:marinespecies.org:taxname:7 Other N Not well described, clusted flagellates Posssibly Synura?  
Cochlodinium 10 Margalefidinium polykrikoides 990876 urn:lsid:marinespecies.org:taxname:990876 Dinoflagellate Y Named was updated, but class name has not been updated.    
Corethron 11 Corethron 149109 urn:lsid:marinespecies.org:taxname:149109 Diatom N Diatom, Need to check if species can be resolve    
Cryptophyte 12 Cryptophyte 17638 urn:lsid:marinespecies.org:taxname:17638 Other N Biflagellate, with ejectsomes Small teardrop shaped  
Cyl_Nitz 13 Nitzschia/Cylindrotheca 149002 urn:lsid:marinespecies.org:taxname:149002 Diatom N Combindation of the two genera, Nitzschia and Cylindrotheca Pennate with distinct rounded center + spines, not uniform thickness.  
Det_Cer_Lau 14 Detonula, Cerataulina, Lauderia 148899 urn:lsid:marinespecies.org:taxname:148899 Diatom N Square or rectangular cells. Chain or single celled If chains, cells must be touching. if single cells and wider than long, put in Centric  
Dictyocha 15 Dictocha 157258 urn:lsid:marinespecies.org:taxname:157258 Other N Silicoflagellate    
Dinophysis 16 Dinophysis 19542 urn:lsid:marinespecies.org:taxname:19542 Dinoflagellate Y Morphologies are not currently disentangled Rounded bottom and two “fins”  
Ditylum 17 Ditylum 149022 urn:lsid:marinespecies.org:taxname:149022 Diatom N Large rolling-pin shaped diatom Can be triangular in cross section.  
Entomoneis 18 Entomoneis 156598 urn:lsid:marinespecies.org:taxname:156598 Diatom N Common in SF Bay butterfly-shaped diatom, “fins” are transparent and sometimes out of frame  
Eucampia 19 Eucampia 616809 urn:lsid:marinespecies.org:taxname:616809 Diatom N Ecuampia zoodiacus, bloom forming    
FlagMix 20 Flagellates 1 urn:lsid:marinespecies.org:taxname:1 Other N Catch all Flagellate, generally not enough resolution to any flagellates except Pyramimonas  
Guin_Dact 21 Guinardia/Dactyliosolen 149068 urn:lsid:marinespecies.org:taxname:616811 Diatom N Curved cells as opposed to Detonula, Cerataulina, Lauderia
Cells must be curved. if straight, put in det_cer_lau
 
Gymnodinium 22 Gymnodinium 109475 urn:lsid:marinespecies.org:taxname:109475 Dinoflagellate Y Many species    
Gyrodinium 23 Gyrodinium 109476 urn:lsid:marinespecies.org:taxname:109476 Dinoflagellate N      
Hemiaulus 24 Hemiaulus 163248 urn:lsid:marinespecies.org:taxname:163248 Diatom N Not to be confused with Eucampia. Straight in valve view, curved in girdle view. Can have slightly convex ends, or straighter ends with horns  
Leptocylindrus 25 Leptocylindrus 149038 urn:lsid:marinespecies.org:taxname:149038 Diatom N      
Licmophora 26 Licmophora 149342 urn:lsid:marinespecies.org:taxname:149342 Diatom N      
Lingulodinium 27 Lingulodinium 231799 urn:lsid:marinespecies.org:taxname:231799 Dinoflagellate Y      
Mesodinium 28 Mesodinium 232069 urn:lsid:marinespecies.org:taxname:232069 Cilliate N Mesodinium rubrum. Orientation can make this hard to distinguish from other cilliates.  
NanoP_less10 29 Nano Plankton, < 10 μm 1 urn:lsid:marinespecies.org:taxname:1 Other N Catch-all group for small (<10 um) cells that can’t be distinguished.    
Odontella 30 Odontella 148963 urn:lsid:marinespecies.org:taxname:148963 Diatom N      
Pennate 31 Pennate Diatom 148899 urn:lsid:marinespecies.org:taxname:148899 Diatom N Single cell (not-chain) pennate diatoms single or rafted pennate cells, includes single pseudos  
Peridinium 32 Peridinium 109549 urn:lsid:marinespecies.org:taxname:109549 Dinoflagellate N Unarmored, dark dinoflagellate. No “feet” Possibly Gymnodinium (unarmoured) but we’ve been putting them here.  
Phaeocystis 33 Phaeocystis 115088 urn:lsid:marinespecies.org:taxname:115088 Other N clusters of small cells    
Pleurosigma 34 Pleurosigma 149181 urn:lsid:marinespecies.org:taxname:149181 Other Y      
Polykrikos 35 Polykrikos 109485 urn:lsid:marinespecies.org:taxname:109485 Dinoflagellate N      
Prorocentrum 36 Prorocentrum 109566 urn:lsid:marinespecies.org:taxname:109566 Dinoflagellate Y      
Protoperidinium 37 Protoperidinium 109553 urn:lsid:marinespecies.org:taxname:109553 Dinoflagellate Y      
Pseudo-nitzschia 38 Pseudo-nitzschia 149151 urn:lsid:marinespecies.org:taxname:149151 Diatom Y      
Pyramimonas 39 Pyramimonas 134529 urn:lsid:marinespecies.org:taxname:134529 Other N      
Rhiz_Prob 40 Rhizosolenia/Proboscia 149068 urn:lsid:marinespecies.org:taxname:149068 Diatom N      
Scrip_Het 41 Scrippsiella/Heterocapsa 109394 urn:lsid:marinespecies.org:taxname:109394 Dinoflagellate N      
Skeletonema 42 Skeletonema 149073 urn:lsid:marinespecies.org:taxname:149073 Diatom N      
Thalassionema 43 Thalassionema 149092 urn:lsid:marinespecies.org:taxname:149092 Diatom N Pennate with squared ends, zig zag chains Single cells go in Pennate  
Thalassiosira 44 Thalassiosira 148912 urn:lsid:marinespecies.org:taxname:148912 Diatom N Two or more cells in a chain Single cells go in Centric  
Tiarina 45 Tiarina 247913 urn:lsid:marinespecies.org:taxname:247913 Other N      
Tintinnid 46 Tintinnid 732976 urn:lsid:marinespecies.org:taxname:732976 Cilliate N      
Tontonia 47 Tontonia 101196 urn:lsid:marinespecies.org:taxname:101196 Cilliate N      
Torodinium 48 Torodinium 109479 urn:lsid:marinespecies.org:taxname:109479 Dinoflagellate N Large, blimp-shaped dino    
Tropidoneis 49 Tropidoneis 149518 urn:lsid:marinespecies.org:taxname:149518 Diatom N      
Vicicitus 50 Vicicitus 707571 urn:lsid:marinespecies.org:taxname:707571 Diatom N Round, like a large centric, but lumpy    
unclassified 51 Unclassified   urn:lsid:marinespecies.org:taxname: Other   Classification lacked confidence to asssign a class    

Class-Specific Thresholds

Class-specific thresholds are an important processing step for accounting for bias in the training dataset. Nonuniformity in the training data reflect both practical desicions made by the creators of the data set and the natural distribution of observered phytoplankton classes. In plain terms, the result is that the model is more likely to guess that something belongs to the more commonly observed classes. In that case, we require a high threshold in that predication in order to assign confidence. Conversely when a less common class is observed, it makes sense to have a lower threshold to assign confidence.

Thresholds can be generated for each class by incrementally increasing a threshold from 0 to 1 and calculating the resulting metrics. In this case, the F-score was used to balance recall and percision. The threshold values where F-score begins to decrease (diff > 0.005) are the class-specific thresholds. Thresolds are calculated for each class and are shown in the table below.

Note

Thresholds

REPLACE WITH UP-TO-DATE Each curve shows the accuracy as the threshold is increased (up to .99). The point where the curve begins to decrease is the threshold value for that class.

Class-specific thresholds
Class Name Threshold
Akashiwo 0.95
Alexandrium_singlet 0.49
Amy_Gony_Protoc 0.35
Asterionellopsis 0.56
Boreadinium 0.45
Centric 0.7
Ceratium 0.95
Chaetoceros 0.89
Ciliates 0.49
Clusterflagellate 0.55
Cochlodinium 0.48
Corethron 0.29
Cryptophyte 0.38
Cyl_Nitz 0.56
Det_Cer_Lau 0.52
Dictyocha 0.6
Dinophysis 0.92
Ditylum 0.27
Entomoneis 0.38
Eucampia 0.88
FlagMix 0.81
Guin_Dact 0.37
Gymnodinium 0.42
Gyrodinium 0.63
Hemiaulus 0.47
Leptocylindrus 0.62
Licmophora 0.57
Lingulodinium 0.56
Mesodinium 0.39
NanoP_less10 0.92
Odontella 0.51
Pennate 0.81
Peridinium 0.44
Phaeocystis 0.81
Pleurosigma 0.35
Polykrikos 0.79
Prorocentrum 0.92
Protoperidinium 0.73
Pseudo-nitzschia 0.62
Pyramimonas 0.4
Rhiz_Prob 0.47
Scrip_Het 0.71
Skeletonema 0.43
Thalassionema 0.62
Thalassiosira 0.36
Tiarina 0.44
Tintinnid 0.94
Tontonia 0.46
Torodinium 0.49
Tropidoneis 0.45
Vicicitus 0.41