Imports:

# All Imports
import os
from matplotlib import pyplot as plt
import pandas as pd
from sklearn.calibration import LabelEncoder
import seaborn as sns
import matplotlib.image as mpimg
import cv2
import numpy as np
import pickle

# Tensflor and Keras Layer and Model and Optimize and Loss
import tensorflow as tf
from tensorflow import keras
from keras import Sequential
from keras.layers import *

#Kernel Intilizer 
from keras.optimizers import Adamax

# PreTrained Model
from keras.applications import *

#Early Stopping
from keras.callbacks import EarlyStopping
import warnings 

Warnings Suppression | Configuration

# Warnings Remove 
warnings.filterwarnings("ignore")

# Define the base path for the training folder
base_path = 'jaguar_cheetah/train'

# Weights file
weights_file = 'Model_train_weights.weights.h5'

# Path to the saved or to save the model:
model_file = 'Model-cheetah_jaguar_Treined.keras'

# Model history
history_path = 'training_history_cheetah_jaguar.pkl'

# Initialize lists to store file paths and labels
filepaths = []
labels = []

# Iterate over folders and files within the training directory
for folder in ['Cheetah', 'Jaguar']:
  folder_path = os.path.join(base_path, folder)
  for filename in os.listdir(folder_path):
    file_path = os.path.join(folder_path, filename)
    filepaths.append(file_path)
    labels.append(folder)

# Create the TRAINING dataframe
file_path_series = pd.Series(filepaths , name= 'filepath')
Label_path_series = pd.Series(labels , name = 'label')
df_train = pd.concat([file_path_series ,Label_path_series ] , axis = 1)


# Define the base path for the test folder
directory = "jaguar_cheetah/test"

filepath =[]
label = []

folds = os.listdir(directory)

for fold in folds:
  f_path = os.path.join(directory , fold)
  
  imgs = os.listdir(f_path)
  
  for img in imgs:
    
    img_path = os.path.join(f_path , img)
    filepath.append(img_path)
    label.append(fold)
    
# Create the TEST dataframe
file_path_series = pd.Series(filepath , name= 'filepath')
Label_path_series = pd.Series(label , name = 'label')
df_test = pd.concat([file_path_series ,Label_path_series ] , axis = 1)

# Display the first rows of the dataframe for verification
#print(df_train)

# Folders with Training and Test files
data_dir = 'jaguar_cheetah/train'
test_dir = 'jaguar_cheetah/test'

# Image size 256x256
IMAGE_SIZE = (256,256) 

Tain | Test

#print('Training Images:')

# Create the TRAIN dataframe
train_ds = tf.keras.utils.image_dataset_from_directory(
  data_dir,
  validation_split=0.1,
  subset='training',
  seed=123,
  image_size=IMAGE_SIZE,
  batch_size=32)

#Testing Data
#print('Validation Images:')
validation_ds = tf.keras.utils.image_dataset_from_directory(
  data_dir, 
  validation_split=0.1,
  subset='validation',
  seed=123,
  image_size=IMAGE_SIZE,
  batch_size=32)

print('Testing Images:')
test_ds = tf.keras.utils.image_dataset_from_directory(
  test_dir, 
  seed=123,
  image_size=IMAGE_SIZE,
  batch_size=32)

# Extract labels
train_labels = train_ds.class_names
test_labels = test_ds.class_names
validation_labels = validation_ds.class_names

# Encode labels
# Defining the class labels
class_labels = ['CHEETAH', 'JAGUAR'] 

# Instantiate (encoder) LabelEncoder
label_encoder = LabelEncoder()

# Fit the label encoder on the class labels
label_encoder.fit(class_labels)

# Transform the labels for the training dataset
train_labels_encoded = label_encoder.transform(train_labels)

# Transform the labels for the validation dataset
validation_labels_encoded = label_encoder.transform(validation_labels)

# Transform the labels for the testing dataset
test_labels_encoded = label_encoder.transform(test_labels)

# Normalize the pixel values

# Train files 
train_ds = train_ds.map(lambda x, y: (x / 255.0, y))
# Validate files
validation_ds = validation_ds.map(lambda x, y: (x / 255.0, y))
# Test files
test_ds = test_ds.map(lambda x, y: (x / 255.0, y))

#TRAINING VISUALIZATION
#Count the occurrences of each category in the column
count = df_train['label'].value_counts()

# Create a figure with 2 subplots
fig, axs = plt.subplots(1, 2, figsize=(12, 6), facecolor='white')

# Plot a pie chart on the first subplot
palette = sns.color_palette("viridis")
sns.set_palette(palette)
axs[0].pie(count, labels=count.index, autopct='%1.1f%%', startangle=140)
axs[0].set_title('Distribution of Training Categories')

# Plot a bar chart on the second subplot
sns.barplot(x=count.index, y=count.values, ax=axs[1], palette="viridis")
axs[1].set_title('Count of Training Categories')

# Adjust the layout
plt.tight_layout()

# Visualize
plt.show()

# TEST VISUALIZATION
count = df_test['label'].value_counts()

# Create a figure with 2 subplots
fig, axs = plt.subplots(1, 2, figsize=(12, 6), facec...

Open Images is a dataset of ~9M images that have been annotated with image-level labels and object bounding boxes.

The training set of V4 contains 14.6M bounding boxes for 600 object classes on 1.74M images, making it the largest existing dataset with object location annotations. The boxes have been largely manually drawn by professional annotators to ensure accuracy and consistency. The images are very diverse and often contain complex scenes with several objects (8.4 per image on average). Moreover, the dataset is annotated with image-level labels spanning thousands of classes.

To use this dataset:

import tensorflow_datasets as tfds

ds = tfds.load('open_images_v4', split='train')
for ex in ds.take(4):
 print(ex)

See the guide for more informations on tensorflow_datasets.

https://storage.googleapis.com/tfds-data/visualization/fig/open_images_v4-original-2.0.0.png" alt="Visualization" width="500px">

Here is a short description of a project that uses OpenCV in Python to process images:

Load an image: You can use the cv2.imread function to load an image into memory.

Pre-processing: Depending on your requirements, you can perform various operations on the image such as resizing, cropping, thresholding, or color conversion.

Image analysis: You can apply various image processing techniques like edge detection, feature extraction, object detection, or template matching to the pre-processed image.

Display results: After processing the image, you can display the results using the cv2.imshow function. You can also save the results to an image file using the cv2.imwrite function.

This project can be used for various applications such as object recognition, facial detection, image segmentation, and more. The implementation details and the algorithms used depend on the specific requirements of the project.

The dataset contains two files in h5 format: 1. test_catvnoncat.h5: It contains 50 test examples of cat and non-cat images 2. train_catvnoncat.h5: It contains 209 train examples of cat and non-cat images

The dataset contains images of size 64x64. The task is to classify an image as a cat (1) or not a cat (0). I am going to publish a series of notebooks for this dataset that would demonstrate neural networks from very basic level. Each notebook will build upon the previous one. Stay tuned to learn neural networks with the help of those notebooks!

You can use the below code snippet to load and visualize the dataset. ```python import numpy as np import matplotlib.pyplot as plt import h5py import os

for dirname, _, filenames in os.walk('/kaggle/input'): for filename in filenames: print(os.path.join(dirname, filename))

def load_data(): train_dataset = h5py.File('/kaggle/input/cat-images-classification-dataset/train_catvnoncat.h5', "r") train_set_x_orig = np.array(train_dataset["train_set_x"][:]) # your train set features train_set_y_orig = np.array(train_dataset["train_set_y"][:]) # your train set labels

test_dataset = h5py.File('/kaggle/input/cat-images-classification-dataset/test_catvnoncat.h5', "r")
test_set_x_orig = np.array(test_dataset["test_set_x"][:]) # your test set features
test_set_y_orig = np.array(test_dataset["test_set_y"][:]) # your test set labels

classes = np.array(test_dataset["list_classes"][:]) # the list of classes

train_set_y_orig = train_set_y_orig.reshape((1, train_set_y_orig.shape[0]))
test_set_y_orig = test_set_y_orig.reshape((1, test_set_y_orig.shape[0]))

return train_set_x_orig, train_set_y_orig, test_set_x_orig, test_set_y_orig, classes

load data

train_x_orig, train_y, test_x_orig, test_y, classes = load_data()

visualize an example image

index = 10 plt.imshow(train_x_orig[index]) print ("y = " + str(train_y[0,index]) + ". It's a " + classes[train_y[0,index]].decode("utf-8") + " picture.") ```

The Oxford-IIIT pet dataset is a 37 category pet image dataset with roughly 200 images for each class. The images have large variations in scale, pose and lighting. All images have an associated ground truth annotation of breed and species. Additionally, head bounding boxes are provided for the training split, allowing using this dataset for simple object detection tasks. In the test split, the bounding boxes are empty.

To use this dataset:

import tensorflow_datasets as tfds

ds = tfds.load('oxford_iiit_pet', split='train')
for ex in ds.take(4):
 print(ex)

See the guide for more informations on tensorflow_datasets.

Python Copilot Image Training using Import Knowledge Graphs

This dataset is a subset of the matlok python copilot datasets. Please refer to the Multimodal Python Copilot Training Overview for more details on how to use this dataset.

  Details

Each row contains a png file in the dbytes column.

Rows: 216642 Size: 211.2 GB Data type: png Format: Knowledge graph using NetworkX with alpaca text box

  Schema

The png is in the dbytes column: { "dbytes": "binary"… See the full description on the dataset page: https://huggingface.co/datasets/matlok/python-image-copilot-training-using-import-knowledge-graphs.

The CIFAR-10 and CIFAR-100 datasets are labeled subsets of the 80 million tiny images dataset. CIFAR-10 and CIFAR-100 were created by Alex Krizhevsky, Vinod Nair, and Geoffrey Hinton. (Sadly, the 80 million tiny images dataset has been thrown into the memory hole by its authors. Spotting the doublethink which was used to justify its erasure is left as an exercise for the reader.)

The CIFAR-10 dataset consists of 60000 32x32 colour images in 10 classes, with 6000 images per class. There are 50000 training images and 10000 test images.

The dataset is divided into five training batches and one test batch, each with 10000 images. The test batch contains exactly 1000 randomly-selected images from each class. The training batches contain the remaining images in random order, but some training batches may contain more images from one class than another. Between them, the training batches contain exactly 5000 images from each class.

The classes are completely mutually exclusive. There is no overlap between automobiles and trucks. "Automobile" includes sedans, SUVs, things of that sort. "Truck" includes only big trucks. Neither includes pickup trucks.

Baseline results You can find some baseline replicable results on this dataset on the project page for cuda-convnet. These results were obtained with a convolutional neural network. Briefly, they are 18% test error without data augmentation and 11% with. Additionally, Jasper Snoek has a new paper in which he used Bayesian hyperparameter optimization to find nice settings of the weight decay and other hyperparameters, which allowed him to obtain a test error rate of 15% (without data augmentation) using the architecture of the net that got 18%.

Other results Rodrigo Benenson has collected results on CIFAR-10/100 and other datasets on his website; click here to view.

Dataset layout Python / Matlab versions I will describe the layout of the Python version of the dataset. The layout of the Matlab version is identical.

The archive contains the files data_batch_1, data_batch_2, ..., data_batch_5, as well as test_batch. Each of these files is a Python "pickled" object produced with cPickle. Here is a python2 routine which will open such a file and return a dictionary: python def unpickle(file): import cPickle with open(file, 'rb') as fo: dict = cPickle.load(fo) return dict And a python3 version: def unpickle(file): import pickle with open(file, 'rb') as fo: dict = pickle.load(fo, encoding='bytes') return dict Loaded in this way, each of the batch files contains a dictionary with the following elements: data -- a 10000x3072 numpy array of uint8s. Each row of the array stores a 32x32 colour image. The first 1024 entries contain the red channel values, the next 1024 the green, and the final 1024 the blue. The image is stored in row-major order, so that the first 32 entries of the array are the red channel values of the first row of the image. labels -- a list of 10000 numbers in the range 0-9. The number at index i indicates the label of the ith image in the array data.

The dataset contains another file, called batches.meta. It too contains a Python dictionary object. It has the following entries: label_names -- a 10-element list which gives meaningful names to the numeric labels in the labels array described above. For example, label_names[0] == "airplane", label_names[1] == "automobile", etc. Binary version The binary version contains the files data_batch_1.bin, data_batch_2.bin, ..., data_batch_5.bin, as well as test_batch.bin. Each of these files is formatted as follows: <1 x label><3072 x pixel> ... <1 x label><3072 x pixel> In other words, the first byte is the label of the first image, which is a number in the range 0-9. The next 3072 bytes are the values of the pixels of the image. The first 1024 bytes are the red channel values, the next 1024 the green, and the final 1024 the blue. The values are stored in row-major order, so the first 32 bytes are the red channel values of the first row of the image.

Each file contains 10000 such 3073-byte "rows" of images, although there is nothing delimiting the rows. Therefore each file should be exactly 30730000 bytes long.

There is another file, called batches.meta.txt. This is an ASCII file that maps numeric labels in the range 0-9 to meaningful class names. It is merely a list of the 10 class names, one per row. The class name on row i corresponds to numeric label i.

The CIFAR-100 dataset This dataset is just like the CIFAR-10, except it has 100 classes containing 600 images each. There are 500 training images and 100 testing images per class. The 100 classes in the CIFAR-100 are grouped into 20 superclasses. Each image comes with a "fine" label (the class to which it belongs) and a "coarse" label (the superclass to which it belongs). Her...

From the paper: We collected a 5003 image dataset automatically from popular Hollywood movies. The images were obtained by running a state-of-the-art person detector on every tenth frame of 30 movies. People detected with high confidence (roughly 20K candidates) were then sent to the crowdsourcing marketplace Amazon Mechanical Turk to obtain groundtruthlabeling. Each image was annotated by five Turkers for $0.01 each to label 10 upperbody joints. The median-of-five labeling was taken in each image to be robust to outlier annotation. Finally, images were rejected manually by us if the person was occluded or severely non-frontal. We set aside 20% (1016 images) of the data for testing.

To use this dataset:

import tensorflow_datasets as tfds

ds = tfds.load('flic', split='train')
for ex in ds.take(4):
 print(ex)

See the guide for more informations on tensorflow_datasets.

https://storage.googleapis.com/tfds-data/visualization/fig/flic-small-2.0.0.png" alt="Visualization" width="500px">

Summary

This dataset contains two hyperspectral and one multispectral anomaly detection images, and their corresponding binary pixel masks. They were initially used for real-time anomaly detection in line-scanning, but they can be used for any anomaly detection task.

They are in .npy file format (will add tiff or geotiff variants in the future), with the image datasets being in the order of (height, width, channels). The SNP dataset was collected using sentinelhub, and the Synthetic dataset was collected from AVIRIS. The Python code used to analyse these datasets can be found at: https://github.com/WiseGamgee/HyperAD

How to Get Started

All that is needed to load these datasets is Python (preferably 3.8+) and the NumPy package. Example code for loading the Beach Dataset if you put it in a folder called "data" with the python script is:

import numpy as np

Load image file

hsi_array = np.load("data/beach_hsi.npy") n_pixels, n_lines, n_bands = hsi_array.shape print(f"This dataset has {n_pixels} pixels, {n_lines} lines, and {n_bands}.")

Load image mask

mask_array = np.load("data/beach_mask.npy") m_pixels, m_lines = mask_array.shape print(f"The corresponding anomaly mask is {m_pixels} pixels by {m_lines} lines.")

Citing the Datasets

If you use any of these datasets, please cite the following paper:

@article{garske2024erx, title={ERX - a Fast Real-Time Anomaly Detection Algorithm for Hyperspectral Line-Scanning}, author={Garske, Samuel and Evans, Bradley and Artlett, Christopher and Wong, KC}, journal={arXiv preprint arXiv:2408.14947}, year={2024},}

If you use the beach dataset please cite the following paper as well (original source):

@article{mao2022openhsi, title={OpenHSI: A complete open-source hyperspectral imaging solution for everyone}, author={Mao, Yiwei and Betters, Christopher H and Evans, Bradley and Artlett, Christopher P and Leon-Saval, Sergio G and Garske, Samuel and Cairns, Iver H and Cocks, Terry and Winter, Robert and Dell, Timothy}, journal={Remote Sensing}, volume={14}, number={9}, pages={2244}, year={2022}, publisher={MDPI} }

South Park

  South Park Images Dataset








  Installation

from huggingface_hub import snapshot_download

repo_id = "asigalov61/South-Park" repo_type = 'dataset'

local_dir = "./South-Park"

snapshot_download(repo_id, repo_type=repo_type, local_dir=local_dir)

  Make your own dataset

!pip install opencv-python

import cv2 import os from tqdm import tqdm

===============================================================================================def… See the full description on the dataset page: https://huggingface.co/datasets/asigalov61/South-Park.

Upload From Python

## Overview

Upload From Python is a dataset for object detection tasks - it contains Cars WyfR annotations for 3,002 images.

## Getting Started

You can download this dataset for use within your own projects, or fork it into a workspace on Roboflow to create your own model.

  ## License

  This dataset is available under the [CC BY 4.0 license](https://creativecommons.org/licenses/CC BY 4.0).

Image Processing in Python for 3D image stacks, or imppy3d, is a software repository comprising mostly Python scripts that simplify post-processing and 3D shape characterization of grayscale image stacks, otherwise known as volume-based images, 3D images, or voxel models. imppy3d was originally created for post-processing image stacks generated from X-ray computed tomography measurements. However, imppy3d also contains a functions to aid in post-processing general 2D/3D images. Python was chosen for this library because of it is a productive, easy-to-use language. However, for computationally intense calculations, compiled codes and libraries are used for improved performance, such as well known libraries like Numpy and SciKit-Image. Compiled libraries internal to imppy3d were created using Cython. imppy3d was developed in an Anaconda environment with Windows 10 and Linux in mind, and suitable Anaconda environment files for these operating systems are provided to simplify the process of installing the necessary dependencies. Some of the highlighted capabilities of imppy3d include: interactive graphical user-interfaces (GUIs) available for many image processing functions, various 2D/3D image filters (e.g., blurring, sharpening, denoising, erosion/dilation), the ability to segment and label continuous 3D objects, precisely rotating an image stack in 3D and re-slicing along the new Z-axis, multiple algorithms for fitting rotated bounding boxes to continuous voxel objects, and export options to convert image stacks into 3D voxel models or smooth surface-based STL models suitable for viewing in ParaView. Additional information and example scripts can be found in the included ReadMe files. Version 1.0 of imppy3d is included here for download, but for the most up to date version of imppy3d, visit the official NIST GitHub repository at, https://github.com/usnistgov/imppy3d LICENSE NIST-developed software is provided by NIST as a public service. You may use, copy, and distribute copies of the software in any medium, provided that you keep intact this entire notice. You may improve, modify, and create derivative works of the software or any portion of the software, and you may copy and distribute such modifications or works. Modified works should carry a notice stating that you changed the software and should note the date and nature of any such change. Please explicitly acknowledge the National Institute of Standards and Technology as the source of the software. NIST-developed software is expressly provided "AS IS." NIST MAKES NO WARRANTY OF ANY KIND, EXPRESS, IMPLIED, IN FACT, OR ARISING BY OPERATION OF LAW, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTY OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NON-INFRINGEMENT, AND DATA ACCURACY. NIST NEITHER REPRESENTS NOR WARRANTS THAT THE OPERATION OF THE SOFTWARE WILL BE UNINTERRUPTED OR ERROR-FREE, OR THAT ANY DEFECTS WILL BE CORRECTED. NIST DOES NOT WARRANT OR MAKE ANY REPRESENTATIONS REGARDING THE USE OF THE SOFTWARE OR THE RESULTS THEREOF, INCLUDING BUT NOT LIMITED TO THE CORRECTNESS, ACCURACY, RELIABILITY, OR USEFULNESS OF THE SOFTWARE. You are solely responsible for determining the appropriateness of using and distributing the software and you assume all risks associated with its use, including but not limited to the risks and costs of program errors, compliance with applicable laws, damage to or loss of data, programs or equipment, and the unavailability or interruption of operation. This software is not intended to be used in any situation where a failure could cause risk of injury or damage to property. The software developed by NIST employees is not subject to copyright protection within the United States.

The Robomimic machine generated datasets were collected using a Soft Actor Critic agent trained with a dense reward. Each dataset consists of the agent's replay buffer.

Each task has two versions: one with low dimensional observations (low_dim), and one with images (image).

The datasets follow the RLDS format to represent steps and episodes.

To use this dataset:

import tensorflow_datasets as tfds

ds = tfds.load('robomimic_mg', split='train')
for ex in ds.take(4):
 print(ex)

See the guide for more informations on tensorflow_datasets.

The Voxel dataset is a constructed dataset of 3D shapes designed to present a unique problem for ML and NAS tools. Instead of a photo of a 3D object, we exploit ML's ability to work across N number of 'colour' channels and use this dimension as a third dimension for images. This dataset is one of the three hidden datasets used by the 2024 NAS Unseen-Data Challenge. The images include 70,000 generated 3D Images of seven different shapes that we generated by creating a 20x20x20 grid of points in 3d space, and randomly generated different 3D shapes (see below) and recorded which of the points the shape collided with, generating the voxel like shapes in the dataset. The data has a shape of (n, 20, 20, 20) where n is the number of samples in the corresponding set (50,000 for training, 10,000 for validation, and 10,000 for testing). For each class (shape), we generated 10,000 samples evenly distributed between the three sets. The three classes and corresponding numerical labels are as follows: Sphere: 0, Cube: 1, Cone: 2, Cylinder: 3, Ellipsoid: 4, Cuboid: 5, Pyramid: 6

NumPy (.npy) files can be opened through the NumPy Python library, using the numpy.load() function by inputting the path to the file into the function as a parameter. The metadata file contains some basic information about the datasets, and can be opened in many text editors such as vim, nano, notepad++, notepad, etc

OSCAR, the Occluded Stereo dataset for Convolutional Architectures with Recurrence. Version: 2.0
(dataset as presented in our JOV 2021 journal publication "Recurrent Processing Improves Occluded Object Recognition and Gives Rise to Perceptual Hysteresis")

If you make use of the dataset, please cite as follows:

Ernst, M. R., Burwick, T., & Triesch, J. (2021). Recurrent Processing Improves Occluded Object Recognition and Gives Rise to Perceptual Hysteresis. In Journal of Vision

Contents

• readme.md - detailed description and sample pictures
• img.zip - folder that contains images for the readme file
• licence.md - licence agreement for using the datasets
• os-fmnist2c.zip - compressed archive of the occluded stereo FashionMNIST dataset (centered, ~1.1GB)
• os-fmnist2r.zip - compressed archive of the occluded stereo FashionMNIST dataset (random, ~1.2GB)
• os-mnist2c.zip - compressed archive of the occluded stereo MNIST dataset (centered, ~865MB)
• os-mnist2r.zip - compressed archive of the occluded stereo MNIST dataset (random, ~851MB)
• os-ycb2.zip - compressed archive of the occluded stereo ycb-object dataset (~1.1GB)
• os-ycb2_highres.zip - compressed archive of the occluded stereo ycb-object dataset (high resolution, ~9.8GB)
• OSCARv2_dataset.py - python script to directly load image data from folder, pytorch dataset

General

For more details and the most up-to-date information please consult our project page: https://kainmueller-lab.github.io/fisbe.

Summary

A new dataset for neuron instance segmentation in 3d multicolor light microscopy data of fruit fly brains

30 completely labeled (segmented) images

71 partly labeled images

altogether comprising ∼600 expert-labeled neuron instances (labeling a single neuron takes between 30-60 min on average, yet a difficult one can take up to 4 hours)

To the best of our knowledge, the first real-world benchmark dataset for instance segmentation of long thin filamentous objects

A set of metrics and a novel ranking score for respective meaningful method benchmarking

An evaluation of three baseline methods in terms of the above metrics and score

Abstract

Instance segmentation of neurons in volumetric light microscopy images of nervous systems enables groundbreaking research in neuroscience by facilitating joint functional and morphological analyses of neural circuits at cellular resolution. Yet said multi-neuron light microscopy data exhibits extremely challenging properties for the task of instance segmentation: Individual neurons have long-ranging, thin filamentous and widely branching morphologies, multiple neurons are tightly inter-weaved, and partial volume effects, uneven illumination and noise inherent to light microscopy severely impede local disentangling as well as long-range tracing of individual neurons. These properties reflect a current key challenge in machine learning research, namely to effectively capture long-range dependencies in the data. While respective methodological research is buzzing, to date methods are typically benchmarked on synthetic datasets. To address this gap, we release the FlyLight Instance Segmentation Benchmark (FISBe) dataset, the first publicly available multi-neuron light microscopy dataset with pixel-wise annotations. In addition, we define a set of instance segmentation metrics for benchmarking that we designed to be meaningful with regard to downstream analyses. Lastly, we provide three baselines to kick off a competition that we envision to both advance the field of machine learning regarding methodology for capturing long-range data dependencies, and facilitate scientific discovery in basic neuroscience.

Dataset documentation:

We provide a detailed documentation of our dataset, following the Datasheet for Datasets questionnaire:

FISBe Datasheet

Our dataset originates from the FlyLight project, where the authors released a large image collection of nervous systems of ~74,000 flies, available for download under CC BY 4.0 license.

Files

fisbe_v1.0_{completely,partly}.zip

contains the image and ground truth segmentation data; there is one zarr file per sample, see below for more information on how to access zarr files.

fisbe_v1.0_mips.zip

maximum intensity projections of all samples, for convenience.

sample_list_per_split.txt

a simple list of all samples and the subset they are in, for convenience.

view_data.py

a simple python script to visualize samples, see below for more information on how to use it.

dim_neurons_val_and_test_sets.json

a list of instance ids per sample that are considered to be of low intensity/dim; can be used for extended evaluation.

Readme.md

general information

How to work with the image files

Each sample consists of a single 3d MCFO image of neurons of the fruit fly.For each image, we provide a pixel-wise instance segmentation for all separable neurons.Each sample is stored as a separate zarr file (zarr is a file storage format for chunked, compressed, N-dimensional arrays based on an open-source specification.").The image data ("raw") and the segmentation ("gt_instances") are stored as two arrays within a single zarr file.The segmentation mask for each neuron is stored in a separate channel.The order of dimensions is CZYX.

We recommend to work in a virtual environment, e.g., by using conda:

conda create -y -n flylight-env -c conda-forge python=3.9conda activate flylight-env

How to open zarr files

Install the python zarr package:

pip install zarr

Opened a zarr file with:

import zarrraw = zarr.open(, mode='r', path="volumes/raw")seg = zarr.open(, mode='r', path="volumes/gt_instances")

optional:import numpy as npraw_np = np.array(raw)

Zarr arrays are read lazily on-demand.Many functions that expect numpy arrays also work with zarr arrays.Optionally, the arrays can also explicitly be converted to numpy arrays.

How to view zarr image files

We recommend to use napari to view the image data.

Install napari:

pip install "napari[all]"

Save the following Python script:

import zarr, sys, napari

raw = zarr.load(sys.argv[1], mode='r', path="volumes/raw")gts = zarr.load(sys.argv[1], mode='r', path="volumes/gt_instances")

viewer = napari.Viewer(ndisplay=3)for idx, gt in enumerate(gts): viewer.add_labels( gt, rendering='translucent', blending='additive', name=f'gt_{idx}')viewer.add_image(raw[0], colormap="red", name='raw_r', blending='additive')viewer.add_image(raw[1], colormap="green", name='raw_g', blending='additive')viewer.add_image(raw[2], colormap="blue", name='raw_b', blending='additive')napari.run()

Execute:

python view_data.py /R9F03-20181030_62_B5.zarr

Metrics

S: Average of avF1 and C

avF1: Average F1 Score

C: Average ground truth coverage

clDice_TP: Average true positives clDice

FS: Number of false splits

FM: Number of false merges

tp: Relative number of true positives

For more information on our selected metrics and formal definitions please see our paper.

Baseline

To showcase the FISBe dataset together with our selection of metrics, we provide evaluation results for three baseline methods, namely PatchPerPix (ppp), Flood Filling Networks (FFN) and a non-learnt application-specific color clustering from Duan et al..For detailed information on the methods and the quantitative results please see our paper.

License

The FlyLight Instance Segmentation Benchmark (FISBe) dataset is licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license.

Citation

If you use FISBe in your research, please use the following BibTeX entry:

@misc{mais2024fisbe, title = {FISBe: A real-world benchmark dataset for instance segmentation of long-range thin filamentous structures}, author = {Lisa Mais and Peter Hirsch and Claire Managan and Ramya Kandarpa and Josef Lorenz Rumberger and Annika Reinke and Lena Maier-Hein and Gudrun Ihrke and Dagmar Kainmueller}, year = 2024, eprint = {2404.00130}, archivePrefix ={arXiv}, primaryClass = {cs.CV} }

Acknowledgments

We thank Aljoscha Nern for providing unpublished MCFO images as well as Geoffrey W. Meissner and the entire FlyLight Project Team for valuablediscussions.P.H., L.M. and D.K. were supported by the HHMI Janelia Visiting Scientist Program.This work was co-funded by Helmholtz Imaging.

Changelog

There have been no changes to the dataset so far.All future change will be listed on the changelog page.

Contributing

If you would like to contribute, have encountered any issues or have any suggestions, please open an issue for the FISBe dataset in the accompanying github repository.

All contributions are welcome!

ImageNet-A is a set of images labelled with ImageNet labels that were obtained by collecting new data and keeping only those images that ResNet-50 models fail to correctly classify. For more details please refer to the paper.

The label space is the same as that of ImageNet2012. Each example is represented as a dictionary with the following keys:

• 'image': The image, a (H, W, 3)-tensor.
• 'label': An integer in the range [0, 1000).
• 'file_name': A unique sting identifying the example within the dataset.

To use this dataset:

import tensorflow_datasets as tfds

ds = tfds.load('imagenet_a', split='train')
for ex in ds.take(4):
 print(ex)

See the guide for more informations on tensorflow_datasets.

https://storage.googleapis.com/tfds-data/visualization/fig/imagenet_a-0.1.0.png" alt="Visualization" width="500px">

This dataset contains 7000 invoice images and their corresponding JSON files. There are 7 types of invoices in this dataset, each one containing 1000 examples each. The data content in the invoices has been generated using Python Faker. If you do not want to download in the form of parquet (default download format) and want to download the dataset in the original format (a folder containing the 2 subfolders, image and json), use the below code: from huggingface_hub import snapshot_download… See the full description on the dataset page: https://huggingface.co/datasets/Ananthu01/7000_invoice_images_with_json.

ImageNet-v2 is an ImageNet test set (10 per class) collected by closely following the original labelling protocol. Each image has been labelled by at least 10 MTurk workers, possibly more, and depending on the strategy used to select which images to include among the 10 chosen for the given class there are three different versions of the dataset. Please refer to section four of the paper for more details on how the different variants were compiled.

The label space is the same as that of ImageNet2012. Each example is represented as a dictionary with the following keys:

• 'image': The image, a (H, W, 3)-tensor.
• 'label': An integer in the range [0, 1000).
• 'file_name': A unique sting identifying the example within the dataset.

To use this dataset:

import tensorflow_datasets as tfds

ds = tfds.load('imagenet_v2', split='train')
for ex in ds.take(4):
 print(ex)

See the guide for more informations on tensorflow_datasets.

https://storage.googleapis.com/tfds-data/visualization/fig/imagenet_v2-matched-frequency-3.0.0.png" alt="Visualization" width="500px">

ILSVRC 2012, commonly known as 'ImageNet' is an image dataset organized according to the WordNet hierarchy. Each meaningful concept in WordNet, possibly described by multiple words or word phrases, is called a "synonym set" or "synset". There are more than 100,000 synsets in WordNet, majority of them are nouns (80,000+). In ImageNet, we aim to provide on average 1000 images to illustrate each synset. Images of each concept are quality-controlled and human-annotated. In its completion, we hope ImageNet will offer tens of millions of cleanly sorted images for most of the concepts in the WordNet hierarchy.

The test split contains 100K images but no labels because no labels have been publicly released. We provide support for the test split from 2012 with the minor patch released on October 10, 2019. In order to manually download this data, a user must perform the following operations:

1. Download the 2012 test split available here.
2. Download the October 10, 2019 patch. There is a Google Drive link to the patch provided on the same page.
3. Combine the two tar-balls, manually overwriting any images in the original archive with images from the patch. According to the instructions on image-net.org, this procedure overwrites just a few images.

The resulting tar-ball may then be processed by TFDS.

To assess the accuracy of a model on the ImageNet test split, one must run inference on all images in the split, export those results to a text file that must be uploaded to the ImageNet evaluation server. The maintainers of the ImageNet evaluation server permits a single user to submit up to 2 submissions per week in order to prevent overfitting.

To evaluate the accuracy on the test split, one must first create an account at image-net.org. This account must be approved by the site administrator. After the account is created, one can submit the results to the test server at https://image-net.org/challenges/LSVRC/eval_server.php The submission consists of several ASCII text files corresponding to multiple tasks. The task of interest is "Classification submission (top-5 cls error)". A sample of an exported text file looks like the following:

771 778 794 387 650
363 691 764 923 427
737 369 430 531 124
755 930 755 59 168

The export format is described in full in "readme.txt" within the 2013 development kit available here: https://image-net.org/data/ILSVRC/2013/ILSVRC2013_devkit.tgz Please see the section entitled "3.3 CLS-LOC submission format". Briefly, the format of the text file is 100,000 lines corresponding to each image in the test split. Each line of integers correspond to the rank-ordered, top 5 predictions for each test image. The integers are 1-indexed corresponding to the line number in the corresponding labels file. See labels.txt.

To use this dataset:

import tensorflow_datasets as tfds

ds = tfds.load('imagenet2012', split='train')
for ex in ds.take(4):
 print(ex)

See the guide for more informations on tensorflow_datasets.

https://storage.googleapis.com/tfds-data/visualization/fig/imagenet2012-5.1.0.png" alt="Visualization" width="500px">