Update README with more info on annotation and sample image

README.md

@@ -93,15 +93,15 @@ The `individual_images` directory contains images of each individual segmented f
 ```
 /dataset/
     group_images/
-        <pictureID 1>.png
-        <pictureID 2>.png
+        <pictureID 1>.jpg
+        <pictureID 2>.jpg
         ...
-        <pictureID 577>.png
+        <pictureID 577>.pg
     individual_images/
-        <individualID 1>.png
-        <individualID 2>.png
+        <individualID 1>.jpg
+        <individualID 2>.jpg
         ...
-        <individualID n>.png
+        <individualID n>.jpg
     BeetleMeasurements.csv
     individual_metadata.csv
 ```
@@ -125,19 +125,20 @@ Ex: All images are named <img_id>.png, each within a folder named for the specie
   - `scalebar`: Pixel coordinates of the ruler/scalebar in the image.
   - `scale_dist_pix`: Integer. The length in pixels of the scalebar.
   - `individual`: Integer. The beetle in the image to whom the measurements refer. Awaiting confirmation of how they are counted.
-  - `structure`: Whether the measurement applies to the length or width of the elytra (`ElytraLength` or `ElytraWidth`, respectively).
+  - `structure`: Whether the measurement applies to the length or width of the elytra (`ElytraLength` or `ElytraWidth`, respectively). 
   - `lyingstraight`: Whether or not the beetle is "straight" in the image (`Yes` or `No`). Further guidance on this term's meaning would be helpful.
   - `coords_pix`: Pixel coordinates of the line marking the length or width of the elytra (green or purple --confirm which is which). Note that the lines are more than one pixel wide, which is why these coordinates form a rectangle.
   - `dist_pix`: Float. The length or width of the elytra (indicated by `structure`) as measured in pixels.
   - `dist_cm`: Float. The length or width of the elytra (indicated by `structure`) as measured in centimeters using the scalebar (the red line in the reference image denotes the pixel count for 1cm).
-  - `scientificName`: Scientific name of the specimen (`<Genus> <species>`). There are 85 different species among 36 genera.
+  - `scientificName`: Scientific name of the specimen (`<Genus> <species>`). There are 85 different species among 36 genera. The 17 individuals in `PictureID` `MOAB_001.S.20180724.jpg` are missing the scientific name label.
+  - `NEON_sampleID_	`: NEON identifier for the sample (576 unique IDs), prefixed by the `plotID`.
   - `siteID`: String. Identifier for the site from which the specimens were collected. There 30 different site IDs.
-  - `field_site_name`: Name of site from which the specimens were collected. There are 43 different field site names.
+  - `field_site_name`: Name of site from which the specimens were collected. There are 43 different field site names. -- These lack consistency, and will be updated using the site codes.
   - `plotID`: Identifier for the plot from which the specimens were collected (`<siteID>_<plot number>`). There are 144 different plots from which specimens were collected.
   - `user_name`: Name of person inputting the information? (`<first><Last>`) or just their username in the system? Only 3 of them. --looks like username
   - `workflow_id`: Integer identifier for the workflow used...?? There are 5.
   - `genus`: Genus of the individual (generated by taking the first word in the `scientificName`).
-  - `individualID`: Unique identifier for the beetles (based on the assumed uniqueness of the `PictureID`, generated from `PictureID` (minus the `.jpg`) plus `_<individual>`.
+  - `individualID`: Unique identifier for the beetles (based on the assumed uniqueness of the `PictureID`), generated from `PictureID` (minus the `.jpg`) plus `_<individual>`. There are 11,104 individuals photographed and annotated.
   - `file_name`: Relative path to image from the root of the directory (`<group_images>/<pictureID>.jpg`); allows for image to be displayed in the dataset viewer alongside its associated metadata.
 
 
@@ -146,11 +147,16 @@ Ex: All images are named <img_id>.png, each within a folder named for the specie
   - `individualID`: ID of beetle in the individual image (matches `individualID` in `BeetleMeasurements.csv`). This is a unique identifier for this CSV.
   - `pictureID`: Name of the group image (`<sample-barcode>.jpg`, though sometimes it's `<NEON_sampleID_>`.jpg). Unique identifier for the 577 _group_ images, not for dataset. (Matches `pictureID` in `BeetleMeasurements.csv`.)
   - `scientificName`: Scientific name of the specimen (`<Genus> <species>`). There are 85 different species among 36 genera.
-  - `elytraLength`: Length of the elytra in centimeters.
-  - `elytraWidth`: Width of the elytra in centimeters.
+  - `elytraLength`: Length of the elytra in centimeters. Indicated by the green line in the image below.
+  - `elytraWidth`: Width of the elytra in centimeters. Indicated by the purple line in the image below.
   - `file_name`: Relative path to image from the root of the directory (`<individual_images>/<individualID>.jpg`); allows for image to be displayed in the dataset viewer alongside its associated metadata.
 
 
+|![Figure 1](https://huggingface.co/datasets/imageomics/BeetlePalooza/resolve/main/beetles.png)|
+|:--|
+|**Figure #.** Sample image of beetles with green and purple lines to indicate the measurement used for the elytra length and width, respectively.|
+
+
 ### Data Splits
 [More Information Needed]
 <!--
@@ -170,7 +176,10 @@ This dataset was curated for use at [BeetlePalooza 2024](https://github.com/Imag
 
 <!-- This section describes the source data (e.g., news text and headlines, social media posts, translated sentences, ...). As well as an original source it was created from (e.g., sampling from Zenodo records, compiling images from different aggregators, etc.) -->
 
-The specimens come from [NEON sites](https://www.neonscience.org/), as indicated in the `BeetleMeasurements` CSV.
+The specimens come from [NEON sites](https://www.neonscience.org/), as indicated in the `BeetleMeasurements` CSV. They were identified by domain scientists (beetle experts) based on physical examination. Each sample consists of a single species. For more information about general NEON data, please see their [Ground beetles sampled from pitfall traps page](https://data.neonscience.org/data-products/DP1.10022.001).
+
+Isa Fluck photographed the beetles in each sample in 2022, using `<fill in camera info>`. 
+
 
 #### Data Collection and Processing
 [More Information Needed]
@@ -192,7 +201,7 @@ If the dataset contains annotations which are not part of the initial data colle
 
 Ex: We standardized the taxonomic labels provided by the various data sources to conform to a uniform 7-rank Linnean structure. (Then, under annotation process, describe how this was done: Our sources used different names for the same kingdom (both _Animalia_ and _Metazoa_), so we chose one for all (_Animalia_). -->
 
-Annotations were completed by 3 individuals (indicated by their NEON system usernames in the `BeetleMeasurements` CSV).
+Annotations (elytra length and width) were completed in Zooniverse by Isa Fluck and two summer REU students (Riley Wolcheski and Isha Chinniah); annotator is indicated by their NEON system usernames in the `BeetleMeasurements` CSV. The annotations were repeated for a subset of the images to measure observation error introduced in the annotation process. Taxonomic labels were provided by NEON with the samples.
 
 #### Annotation process
 [More Information Needed]