DeepCell Label is a web-based tool to visualize and label biological images. It can segment an image, assign cells across a timelapse, and track divisions in multiplexed images, 3D image stacks, and time-lapse movies. ###locally As it's available through a browser, DeepCell Label can crowdsource data labeling or review, correct, and curate labels as a domain expert.
The site is built with React, XState, and Flask and runs locally or on the cloud.
Visit label.deepcell.org to create a project from an example file or your own .tiff, .png, or .npz. Dropdown instructions are available while working on a project in DeepCell Label.
backend/deepcell/
The create_project function has been updated in the @bp.route('/api/project', methods=['POST']) to handle project creation via URL inputs for images and optionally labels. Here's the updated function:
@bp.route('/api/project/<project_id>', methods=['GET'])
def get_project(project_id):
start = timeit.default_timer()
project = Project.get(project_id)
if not project:
return abort(404, description=f'Project {project_id} not found')
file_path = os.path.join('/rsrch5/home/plm/yshokrollahi/project4/apps/deepcell-label/backend', f'{project_id}.zip') # Local path for files
if os.path.exists(file_path):
return send_file(
file_path,
mimetype='application/zip',
as_attachment=True,
attachment_filename=f'{project_id}.zip'
)
else:
return abort(404, description='File not found')
@bp.route('/api/project', methods=['POST'])
def create_project():
"""
Create a new Project from URL.
"""
start = timeit.default_timer()
if 'images' in request.form:
images_url = request.form['images']
else:
return abort(
400,
description='Include "images" in the request form with a URL to download the project data.',
)
labels_url = request.form['labels'] if 'labels' in request.form else None
axes = request.form['axes'] if 'axes' in request.form else None
with tempfile.NamedTemporaryFile(
delete=DELETE_TEMP
) as image_file, tempfile.NamedTemporaryFile(delete=DELETE_TEMP) as label_file:
if images_url is not None:
image_response = requests.get(images_url)
if image_response.status_code != 200:
return (
image_response.text,
image_response.status_code,
image_response.headers.items(),
)
image_file.write(image_response.content)
image_file.seek(0)
if labels_url is not None:
labels_response = requests.get(labels_url)
if labels_response.status_code != 200:
return (
labels_response.text,
labels_response.status_code,
labels_response.headers.items(),
)
label_file.write(labels_response.content)
label_file.seek(0)
else:
label_file = image_file
loader = Loader(image_file, label_file, axes)
project = Project.create(loader)
if not DELETE_TEMP:
image_file.close()
label_file.close()
os.remove(image_file.name) # Manually close and delete if using Windows
current_app.logger.info(
'Created project %s from %s in %s s.',
project.project,
f'{images_url}' if labels_url is None else f'{images_url} and {labels_url}',
timeit.default_timer() - start,
)
return jsonify(project.project)backend/deepcell/
The Project class within the model.py has been updated to handle project creation and data management using SQLAlchemy. The detailed modifications are as follows:
"""SQL Alchemy database models."""
from __future__ import absolute_import, division, print_function
import io
import logging
import timeit
from secrets import token_urlsafe
import boto3
from flask_sqlalchemy import SQLAlchemy
from deepcell_label.config import AWS_ACCESS_KEY_ID, AWS_SECRET_ACCESS_KEY, S3_BUCKET
logger = logging.getLogger('models.Project') # pylint: disable=C0103
db = SQLAlchemy() # pylint: disable=C0103
import os
db = SQLAlchemy()
class Project(db.Model):
"""Project table definition."""
__tablename__ = 'projects'
id = db.Column(db.Integer, primary_key=True, autoincrement=True)
project = db.Column(db.String(12), unique=True, nullable=False, index=True)
createdAt = db.Column(db.TIMESTAMP, nullable=False, default=db.func.now())
# bucket and key columns can be repurposed or removed if not needed
bucket = db.Column(db.Text, nullable=True)
key = db.Column(db.Text, nullable=True)
def __init__(self, loader):
"""
Initialize a new project with data from a loader.
Args:
loader: Loaders.Loader object containing the project data.
"""
start = timeit.default_timer()
# Create a unique 12 character base64 project ID
while True:
project_id = token_urlsafe(9) # 9 bytes is 12 base64 characters
if not db.session.query(Project).filter_by(project=project_id).first():
self.project = project_id
break
# Define local storage path
local_storage_path = '/rsrch5/home/plm/yshokrollahi/project4/apps/deepcell-label/backend'
self.key = f'{self.project}.zip' # Use project ID for the filename
file_path = os.path.join(local_storage_path, self.key)
# Setting a default value for bucket, even if it's not being used
self.bucket = "local"
# Write the project data to a file at the specified path
with open(file_path, 'wb') as file:
file.write(loader.data)
logger.debug(
'Initialized project %s and saved locally to %s in %ss.',
self.project,
file_path,
timeit.default_timer() - start,
)
@staticmethod
def get(project):
"""
Return the project with the given ID, if it exists.
Args:
project (int): unique 12 character base64 string to identify project
Returns:
Project: row from the Project table
"""
start = timeit.default_timer()
project = db.session.query(Project).filter_by(project=project).first()
logger.debug('Got project %s in %ss.', project, timeit.default_timer() - start)
return project
@staticmethod
def create(data):
"""
Create a new project in the Project table.
Args:
data: zip file with loaded project data
Returns:
Project: new row in the Project table
"""
start = timeit.default_timer()
project = Project(data)
db.session.add(project)
db.session.commit()
logger.debug(
'Created new project %s in %ss.',
project.project,
timeit.default_timer() - start,
)
return project