maxsitt/insect-detect-ml

Notebooks for detection and classification model training. Insect classification model. Python scripts for processing of data, collected with the Insect Detect DIY camera trap.

Insect Detect ML - Model training and data processing

This repository contains Jupyter notebooks that can be used to train custom YOLOv5, YOLOv6, YOLOv7 and YOLOv8 object detection models or a custom YOLOv5 image classification model. All notebooks can be run in Google Colab, where you will have access to a free cloud GPU for fast training without special hardware requirements.

The Python script for classification of the captured insect images is available in the custom yolov5 fork and can be used together with the provided insect classification model.

Use the process_metadata.py script for post-processing of metadata .csv files with classification results.

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Model training

You can find more information about detection model training at the Insect Detect Docs 📑.

• YOLOv5 detection model training  

• YOLOv6 detection model training  

• YOLOv7 detection model training  

• YOLOv8 detection model training  

  The PyTorch model weights can be converted to .blob format at tools.luxonis.com for on-device inference with the Luxonis OAK devices.

 

You can find more information about classification model training at the Insect Detect Docs 📑.

• YOLOv5 classification model training  

  The notebook for classification model training includes export to ONNX format for faster CPU inference.

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Classification

The modified classification script in the custom yolov5 fork includes the following added options:

• --sort-top1 sort the classified images to folders with the predicted top1 class as folder name
• --sort-prob sort images first by probability and then by top1 class (requires --sort-top1)
• --concat-csv concatenate all metadata .csv files and append classification results to new columns

More information about deployment of the classification script can be found at the Insect Detect Docs 📑.

 

Classification model

Model (.onnx)	size (pixels)	Top1 Accuracytest	Precisiontest	Recalltest	F1 scoretest
EfficientNet-B0	128	0.972	0.971	0.967	0.969

Table Notes

• The model was trained to 20 epochs with image size 128, batch size 64 and default settings and hyperparameters. Reproduce the model training with the provided Google Colab notebook.
• Trained on Insect Detect - insect classification dataset v2 with 27 classes. To reproduce the dataset split, keep the default settings in the Colab notebook (train/val/test ratio = 0.7/0.2/0.1, random seed = 1).
• Dataset can be explored at Roboflow Universe. Export from Roboflow compresses the images and can lead to a decreased model accuracy. It is recommended to use the uncompressed dataset from Zenodo.

Full model metrics on dataset test split (click to expand)

Class	Images	Top1 Accuracytest	Precisiontest	Recalltest	F1 scoretest
all	2125	0.972	0.971	0.967	0.969
ant	111	1.0	0.991	1.0	0.996
bee	107	0.963	0.972	0.963	0.967
bee_apis	31	1.0	0.969	1.0	0.984
bee_bombus	127	1.0	0.992	1.0	0.996
beetle	52	0.885	0.92	0.885	0.902
beetle_cocci	78	0.987	1.0	0.987	0.994
beetle_oedem	21	0.905	0.905	0.905	0.905
bug	39	0.846	1.0	0.846	0.917
bug_grapho	19	1.0	1.0	1.0	1.0
fly	173	0.971	0.944	0.971	0.957
fly_empi	19	1.0	1.0	1.0	1.0
fly_sarco	33	0.909	0.938	0.909	0.923
fly_small	167	0.958	0.952	0.958	0.955
hfly_episyr	253	0.996	0.996	0.996	0.996
hfly_eristal	197	0.99	0.995	0.99	0.992
hfly_eupeo	137	0.985	0.993	0.985	0.989
hfly_myathr	60	1.0	1.0	1.0	1.0
hfly_sphaero	39	0.974	1.0	0.974	0.987
hfly_syrphus	50	0.98	1.0	0.98	0.99
lepi	24	1.0	0.96	1.0	0.98
none_bg	86	0.988	0.966	0.988	0.977
none_bird	8	1.0	1.0	1.0	1.0
none_dirt	85	0.976	0.902	0.976	0.938
none_shadow	66	0.924	0.953	0.924	0.938
other	79	0.861	0.883	0.861	0.872
scorpionfly	12	1.0	1.0	1.0	1.0
wasp	52	1.0	1.0	1.0	1.0

Full model metrics on dataset validation split (click to expand)

Class	Images	Top1 Accuracyval	Precisionval	Recallval	F1 scoreval
all	4189	0.98	0.979	0.974	0.976
ant	219	0.995	0.995	0.995	0.995
bee	212	0.967	0.958	0.967	0.962
bee_apis	58	1.0	0.967	1.0	0.983
bee_bombus	252	1.0	0.996	1.0	0.998
beetle	104	0.933	0.942	0.933	0.937
beetle_cocci	155	1.0	1.0	1.0	1.0
beetle_oedem	39	0.897	0.972	0.897	0.933
bug	78	0.949	0.961	0.949	0.955
bug_grapho	37	1.0	1.0	1.0	1.0
fly	343	0.983	0.939	0.983	0.96
fly_empi	35	1.0	0.972	1.0	0.986
fly_sarco	63	0.841	0.964	0.841	0.898
fly_small	332	0.97	0.982	0.97	0.976
hfly_episyr	503	0.996	0.996	0.996	0.996
hfly_eristal	390	1.0	1.0	1.0	1.0
hfly_eupeo	271	0.989	0.993	0.989	0.991
hfly_myathr	118	0.992	1.0	0.992	0.996
hfly_sphaero	74	1.0	0.987	1.0	0.993
hfly_syrphus	97	1.0	0.99	1.0	0.995
lepi	45	0.978	0.978	0.978	0.978
none_bg	170	0.988	0.982	0.988	0.985
none_bird	13	1.0	1.0	1.0	1.0
none_dirt	167	0.982	0.976	0.982	0.979
none_shadow	129	0.969	0.984	0.969	0.977
other	158	0.88	0.903	0.88	0.891
scorpionfly	24	1.0	1.0	1.0	1.0
wasp	103	0.99	1.0	0.99	0.995

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Metadata post-processing

Install the required packages by running:

python.exe -m pip install -r requirements.txt

Or use the Python Launcher for Windows with:

py -m pip install -r requirements.txt

The process_metadata.py script can be used to automatically post-process the concatenated metadata .csv file after the classification step, as it will still contain multiple rows for each tracked insect.

The output of the script includes a *top1_final.csv file in which each row corresponds to an individual tracked insect and its classification result with the highest weighted probability. Additionally, several plots are generated that can give a first overview of the processed metadata.

More information about deployment of the post-processing script can be found at the Insect Detect Docs 📑.

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Image processing

The process_images.py script can be used to calculate different metrics of the captured images (e.g. mean/median/min/max width/height) and remove corrupted .jpg images from the data folder (camera trap output). These can be rarely generated by the automated monitoring script (e.g. in power outage situations) and will cause an error while running the classification script.

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License

This repository is licensed under the terms of the GNU Affero General Public License v3.0 (GNU AGPLv3).

Citation

If you use resources from this repository, please cite our paper:

Sittinger M, Uhler J, Pink M, Herz A (2024) Insect detect: An open-source DIY camera trap for automated insect monitoring. PLoS ONE 19(4): e0295474. https://doi.org/10.1371/journal.pone.0295474