Update README.md

README.md

@@ -1,3 +1,59 @@
----
-license: cc-by-nc-sa-4.0
----
+---
+license: cc-by-nc-sa-4.0
+task_categories:
+- image-classification
+tags:
+- biology
+- climate
+pretty_name: AquaMonitor JYU
+size_categories:
+- 10K<n<100K
+---
+
+# AquaMonitor JYU
+
+This is a sample dataset of aquatic invertebrates from 31 classes. The training split has 40,880 images from 1049 individuals, while the validation split has 6394 images from 157 individuals.
+
+# Metadata columns
+
+| Column Name                | Type       | Description |
+|----------------------------|-----------|-------------|
+| img                        | str       | The image filename. Unique identifier across the dataset. |
+| individual                 | str       | Identifier for the individual specimens. |
+| imaging_run                | str       | Identifier for the imaging run. Some specimens have been imaged multiple times, and this ID refers to a single "drop" through the cuvette. Consists of individual id with running number suffix. With bulk imaged samples each individual has been imaged only once, resulting in 'individual' == 'imaging_run'. |
+| taxon                      | str       | The scientific name of the specimen. Refers to both adult and juvenile forms. |
+| taxon_group                | str       | Specifies the visual group of the specimen. Some taxa have specimens from multiple visual groups, like juvenile and adult forms. If the taxon has no such subgroups, this value is the same as 'taxon'. Used for classification benchmarks. |
+| taxon_label                | str       | Original label used during morphological identification. Matches the labels used in the monitoring databases. Was used during imaging and matches image filenames. |
+| taxon_code                 | str       | The abbreviation of the taxon_label. Matches filenames and identifiers. |
+| lake                       | str       | The lake the specimen was collected from. |
+| site                       | str       | Sampling site. |
+| sample                     | str       | The taxon-site combination. Before imaging, the samples were stored in containers with these groupings. |
+| plate                      | str       | (Only on DNA and biomass subsets) The 96 well plate ID. |
+| position                   | str       | (Only on DNA and biomass subsets) The position on the 96 well plate. Values range in [A-H] for rows and [1-12] for columns. |
+| camera                     | int       | The camera the image is from. Values in {1,2}. |
+| area                       | int       | The area of the specimen in the image. From BIODISCOVER imaging software. |
+| perimeter                  | int       | The perimeter of the specimen in the image. From BIODISCOVER imaging software. |
+| holes                      | int       | Number of morphological holes in the image segmentation. From BIODISCOVER imaging software. |
+| max_feret_diameter         | int       | Maximum Feret diameter of the segmentation object. From BIODISCOVER imaging software. |
+| area_holes                 | int       | The area of the morphological holes in the segmentation. From BIODISCOVER imaging software. |
+| roi_left                   | int       | The left position of the image crop, relational to the full cuvette. |
+| roi_top                    | int       | The top position of the image crop, relational to the full cuvette. |
+| roi_right                  | int       | The right position of the image crop, relational to the full cuvette. |
+| roi_bottom                 | int       | The bottom position of the image crop, relational to the full cuvette. |
+| width                      | int       | Width of the image. |
+| height                     | int       | Height of the image. |
+| imaging_time               | datetime  | Imaging timestamp. |
+| dataset                    | str       | The dataset subset image belongs to. Values in {'dna', 'biomass', 'bulk21', 'bulk22'}. |
+| year                       | str       | Sampling year. Values in {'2021', '2022'}. |
+| is_bulk                    | bool      | Whether the image was taken in the bulk imaging phase. |
+| has_dna                    | bool      | The individual has DNA sequence data. |
+| has_biomass                | bool      | The individual has biomass information. |
+| fold0-fold4                | str       | The benchmark split the image belongs to, for five cross-validation folds. Values in {'train', 'val', 'test', '0'}. Values of '0' correspond to images in classes that have less than 50 specimens. |
+| well_col                   | str       | Column in the value 'position'. Values in range [1-12]. |
+| well_row                   | str       | Row in the value 'position'. Values in range [A-H]. |
+| weight                     | float     | Weight of the specimen in milligrams. Calculated from plate_weight and total_weight. |
+| log_weight                 | float     | Natural log of the weight. |
+| log_weight_xplus1          | float     | Weight in the form ln(x+1), where x is the value in 'weight'. |
+| plate_weight               | float     | The measured plate weight. |
+| total_weight               | float     | Weight of the plate with the specimen. |
+| caddisfly_without_shell    | float     | If value is not NaN, this is the total weight of caddisfly samples weighed without the shell. |