Upload folder using huggingface_hub

.gitattributes

@@ -1,59 +1,3 @@
-*.7z filter=lfs diff=lfs merge=lfs -text
-*.arrow filter=lfs diff=lfs merge=lfs -text
-*.bin filter=lfs diff=lfs merge=lfs -text
-*.bz2 filter=lfs diff=lfs merge=lfs -text
-*.ckpt filter=lfs diff=lfs merge=lfs -text
-*.ftz filter=lfs diff=lfs merge=lfs -text
-*.gz filter=lfs diff=lfs merge=lfs -text
-*.h5 filter=lfs diff=lfs merge=lfs -text
-*.joblib filter=lfs diff=lfs merge=lfs -text
-*.lfs.* filter=lfs diff=lfs merge=lfs -text
-*.lz4 filter=lfs diff=lfs merge=lfs -text
-*.mds filter=lfs diff=lfs merge=lfs -text
-*.mlmodel filter=lfs diff=lfs merge=lfs -text
-*.model filter=lfs diff=lfs merge=lfs -text
-*.msgpack filter=lfs diff=lfs merge=lfs -text
-*.npy filter=lfs diff=lfs merge=lfs -text
-*.npz filter=lfs diff=lfs merge=lfs -text
-*.onnx filter=lfs diff=lfs merge=lfs -text
-*.ot filter=lfs diff=lfs merge=lfs -text
-*.parquet filter=lfs diff=lfs merge=lfs -text
-*.pb filter=lfs diff=lfs merge=lfs -text
-*.pickle filter=lfs diff=lfs merge=lfs -text
-*.pkl filter=lfs diff=lfs merge=lfs -text
-*.pt filter=lfs diff=lfs merge=lfs -text
-*.pth filter=lfs diff=lfs merge=lfs -text
-*.rar filter=lfs diff=lfs merge=lfs -text
-*.safetensors filter=lfs diff=lfs merge=lfs -text
-saved_model/**/* filter=lfs diff=lfs merge=lfs -text
-*.tar.* filter=lfs diff=lfs merge=lfs -text
-*.tar filter=lfs diff=lfs merge=lfs -text
-*.tflite filter=lfs diff=lfs merge=lfs -text
-*.tgz filter=lfs diff=lfs merge=lfs -text
-*.wasm filter=lfs diff=lfs merge=lfs -text
-*.xz filter=lfs diff=lfs merge=lfs -text
-*.zip filter=lfs diff=lfs merge=lfs -text
-*.zst filter=lfs diff=lfs merge=lfs -text
-*tfevents* filter=lfs diff=lfs merge=lfs -text
-# Audio files - uncompressed
-*.pcm filter=lfs diff=lfs merge=lfs -text
-*.sam filter=lfs diff=lfs merge=lfs -text
-*.raw filter=lfs diff=lfs merge=lfs -text
-# Audio files - compressed
-*.aac filter=lfs diff=lfs merge=lfs -text
-*.flac filter=lfs diff=lfs merge=lfs -text
-*.mp3 filter=lfs diff=lfs merge=lfs -text
-*.ogg filter=lfs diff=lfs merge=lfs -text
-*.wav filter=lfs diff=lfs merge=lfs -text
-# Image files - uncompressed
-*.bmp filter=lfs diff=lfs merge=lfs -text
-*.gif filter=lfs diff=lfs merge=lfs -text
-*.png filter=lfs diff=lfs merge=lfs -text
-*.tiff filter=lfs diff=lfs merge=lfs -text
-# Image files - compressed
-*.jpg filter=lfs diff=lfs merge=lfs -text
-*.jpeg filter=lfs diff=lfs merge=lfs -text
-*.webp filter=lfs diff=lfs merge=lfs -text
-# Video files - compressed
-*.mp4 filter=lfs diff=lfs merge=lfs -text
-*.webm filter=lfs diff=lfs merge=lfs -text
+metadata/images.csv filter=lfs diff=lfs merge=lfs -text
+metadata/records.csv filter=lfs diff=lfs merge=lfs -text
+images/originals/**/*.jpg filter=lfs diff=lfs merge=lfs -text

.gitignore

@@ -0,0 +1 @@
+.DS_Store

README.md

@@ -0,0 +1,56 @@
+---
+language:
+  - en
+pretty_name: MassID45 Individual Specimens
+description: In this repository, you will find images and metadata for individual specimens in the MassID45 dataset.
+size_categories:
+  - 10K<n<100K
+---
+
+# MassID45 Individual Specimens
+
+MassID45 is a multi-modal dataset comprised of DNA barcodes (COI) and images at two resolutions: of complete bulk insect samples and of the full set of individual specimens from those samples. In this repository, you will find images and metadata for 35,586 individual specimens.
+
+The data for individual specimens is available on BOLD under recordset code [DS-LPEPA22](https://portal.boldsystems.org/recordset/DS-LPEPA22). This HuggingFace dataset makes images easier to access in bulk.
+
+Further information about the MassID45 dataset is available in the pre-print [A multi-modal dataset for insect biodiversity with imagery and DNA at the trap and individual level](https://arxiv.org/abs/2507.06972). Code for preprocessing and training/inference is available at [GitHub](https://github.com/uoguelph-mlrg/MassID45).
+
+## Dataset structure
+
+### Images
+
+The `images` directory contains specimen photographs organized in two resolutions. Images are further organized in sub folders based on bulk sample ids (see column `fieldid` in `metadata/records.csv`).
+
+- **images/originals**: High-resolution images of individual specimens
+- **images/thumbnails**: Lower-resolution thumbnail versions of the same specimens
+
+File path format: `images/[resolution]/[fieldid]/[processid].jpg`
+
+File path example: `images/originals/G1P4N6/LPUAE001-22.jpg`
+
+### Metadata
+
+The `metadata` directory contains two CSV files with record and image information frmo BOLD. The metadata was collected using BOLD APIs and is unmodified.
+
+- **metadata/records.csv**: Detailed metadata for individual specimens
+- **metadata/images.csv**: Image-specific metadata for the same specimens
+
+## Dataset access
+
+To clone this repository, use the following command:
+
+```
+git clone https://huggingface.co/datasets/annaviklund/massid45-specimens/
+```
+
+To exclude large files when cloning, use the following command:
+
+```
+GIT_LFS_SKIP_SMUDGE=1 git clone https://huggingface.co/datasets/annaviklund/massid45-specimens/
+```
+
+## Direct image access
+
+File path format: https://huggingface.co/datasets/annaviklund/massid45-specimens/resolve/main/images/[resolution]/[fieldid]/[processid].jpg
+
+File path example: https://huggingface.co/datasets/annaviklund/massid45-specimens/resolve/main/images/originals/G1P4N6/LPUAE001-22

metadata/images.csv

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:aded4f796b90b1ef7b6b1526d33fefc2f0705d13d4afed9a4a8136982c04ca71
+size 22973116

metadata/records.csv

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:a98dbb903ba748638da2dc70494bccfdfada057a474988a96980b33a475cec63
+size 49285866