clarify individual images in the dataset and point to the code used to create them

README.md

@@ -27,6 +27,10 @@ configs:
 - config_name: resized_images
   data_files:
   - "beetle_images_resized/*.jpg"
+- config_name: separate_segmented
+  data_files:
+  - "Separate_segmented_train_test_splits_80_20/*/*/*.jpg"
+  - "metadata.csv"
 ---
 <!-- - config_name: individual_images
   data_files:
@@ -71,9 +75,17 @@ The individual images were segemented out based on scaling the elytra measuremen
 
 In `group_images` we have 577 images of multiple beetles in a reasonably regular pattern (see sample image below). Each of these images contains a centimeter-based scalebar and a barcode representing the sample (collection of beetles in the image). Each row in `BeetleMeasurements.csv` corresponds to a measurement of the elytra (length or width) of an individual beetle.
 
-The `individual_images` directory contains images of each individual segmented from the group images. These connect back to their group image based on the `individualID`.
+`Separate_segmented_train_test_splits_80_20` contains individual images of 12 different species of beetles. These images are divided into an 80-20 train-test split, and further separated into subfolders based on their species (as shown below).
 
+<!-- Still to be added:
+The `individual_images` directory contains images of each individual segmented from the group images. These connect back to their group image based on the `individualID`.
 
+    individual_images/
+        <individualID 1>.jpg
+        <individualID 2>.jpg
+        ...
+        <individualID 11459>.jpg
+-->
 ```
 /dataset/
     group_images/
@@ -86,11 +98,6 @@ The `individual_images` directory contains images of each individual segmented f
         <pictureID 2>.jpg
         ...
         <pictureID 577>.jpg
-    individual_images/
-        <individualID 1>.jpg
-        <individualID 2>.jpg
-        ...
-        <individualID 11459>.jpg
     Separate_segmented_train_test_splits_80_20
         test/
             <species 1>/
@@ -119,8 +126,11 @@ The `individual_images` directory contains images of each individual segmented f
 
 The `group_images` folder has all 577 orignal full size images. The `beetle_images_resized` folder has the resized (approximately 1MB) images used for annotation in Zooniverse (1MB was the size limitation imposed by the software); aspect ratio was maintained in the resize. <!-- >, and the code used can be found [here](). -->
 
-Segmentation was completed by adapting the elytra length and width annotations to generate the xy point input for the [Segment Anything (SAM)]() model. [Segment Anything (SAM)]() was then used to segment the individual beetles. More information and the code for this process is provided in the [Imageomics/2018-NEON-beetles-processing repo](https://github.com/Imageomics/2018-NEON-beetles-processing).
+The code used to produce the images and splits in `Separate_segmented_train_test_splits_80_20/` is provided [here](https://github.com/Imageomics/2018-NEON-beetles-processing/blob/main/notebooks/Beetle_Palooza_image_separation.ipynb).
 
+<!-- images not provided here
+Segmentation was completed by adapting the elytra length and width annotations to generate the xy point input for the [Segment Anything (SAM)]() model. [Segment Anything (SAM)]() was then used to segment the individual beetles. More information and the code for this process is provided in the [Imageomics/2018-NEON-beetles-processing repo](https://github.com/Imageomics/2018-NEON-beetles-processing).
+-->
 
 |![picture of beetles in A00000046094](https://huggingface.co/datasets/imageomics/BeetlePalooza/resolve/main/group_images/A00000046094.jpg)| 
 |:--|
@@ -169,7 +179,7 @@ Segmentation was completed by adapting the elytra length and width annotations t
   - `file_name`: path to the image from the `Separate_segmented_train_test_splits_80_20` folder to display in the dataset viewer.
   - `subset`: label given to this subset of the full image dataset (as selected in the viewer).
 
-**individual_metadata.csv**:
+**individual_metadata.csv**: This CSV was created for individual images that have not yet been added to this repository.
   - `individualID`: ID of beetle in the individual image (`<measureID_length>_<measureID_width>`). This is a unique identifier for this CSV.
   - `combinedID`: Generated from `PictureID` (minus the `.jpg`) plus `_<individual>`. (Matches `combinedID` in `BeetleMeasurements.csv`.)
   - `lying_flat`: Whether or not the beetle is lying _flat_ in the image (`Yes` or `No`). This does _NOT_ correlate to vertical or horizontal alignment; it is whether the individual is twisted to one side or not--a side effect of how they died. Generally, the measured width will be shorter than the true width if this is `No`.