Fractal tasks for the Opera/Operetta microscope and drug response profiling

Navigation

Verified details

These details have been verified by PyPI
Project links
GitHub Statistics
Maintainers
Avatar for fdsteffen from gravatar.com fdsteffen

Unverified details

These details have not been verified by PyPI
Meta
  • License: BSD-3-Clause
  • Author: Fabio Steffen
  • Requires: Python >=3.10
  • Provides-Extra: dev
Report project as malware

Project description

operetta-compose

Docs Status PyPI

Fractal tasks to convert and process images from Perkin-Elmer Opera/Operetta high-content microscopes. Workflows for drug response profiling built upon the OME-ZARR file standard.

Task library

Currently the following tasks are available:

Task Description
harmony_to_ome_zarr Convert TIFFs which were exported from Harmony (Operetta/Opera, Perkin-Elmer) to OME-ZARR
stardist_segmentation Segment cells with Stardist
regionprops_measurement Take measurements using regionprops and write the features to the OME-ZARR
feature_classification Classify cells using the napari-feature-classifier and write them to the OME-ZARR
condition_registration Register the experimental conditions in the OME-ZARR

Development and installation in Fractal

  1. Install the package in dev mode with python -m pip install -e ".[dev]"
  2. Develop the function according to the Fractal API
  3. Update the image list and the Fractal manifest with fractal-manifest create --package operetta-compose
  4. Build a wheel file in the dist folder of the package with python -m build
  5. Collect the tasks on a Fractal server

Updating docs

  1. Update the documentation under /docs
  2. Update the function API with quartodoc build
  3. Preview the documentation with quarto preview

Fractal is developed by the UZH BioVisionCenter under the lead of @jluethi and under contract with eXact lab S.r.l..

Project details

Verified details

These details have been verified by PyPI
Project links
GitHub Statistics
Maintainers
Avatar for fdsteffen from gravatar.com fdsteffen

Unverified details

These details have not been verified by PyPI
Meta
  • License: BSD-3-Clause
  • Author: Fabio Steffen
  • Requires: Python >=3.10
  • Provides-Extra: dev

Release history Release notifications | RSS feed

This version

0.2.14

0.2.13

0.2.12

0.2.11

0.2.10

0.2.9

0.2.8

0.2.7

0.2.6

0.2.5

0.2.4

0.2.3

0.2.2

0.2.1

0.2.0

0.1.4

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

operetta_compose-0.2.14.tar.gz (20.7 kB view details)

Uploaded Source

Built Distribution

If you're not sure about the file name format, learn more about wheel file names.

operetta_compose-0.2.14-py3-none-any.whl (23.1 kB view details)

Uploaded Python 3

File details

Details for the file operetta_compose-0.2.14.tar.gz.

File metadata

  • Download URL: operetta_compose-0.2.14.tar.gz
  • Upload date:
  • Size: 20.7 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? Yes
  • Uploaded via: twine/6.1.0 CPython/3.13.7

File hashes

Hashes for operetta_compose-0.2.14.tar.gz
Algorithm Hash digest
SHA256 0de6c66ececa6b5c662332a38df5db8898d07e07c64aa69619d8d1ff765d4c08
MD5 31c38f07aebe5e28820af9666d9bad15
BLAKE2b-256 5bf0cb08fb5950127fd0ebaa0a41888f4a200f89b2b55966f5c056c1bb93eb66

See more details on using hashes here.

Provenance

The following attestation bundles were made for operetta_compose-0.2.14.tar.gz:

Publisher: build.yml on leukemia-kispi/operetta-compose

Attestations: Values shown here reflect the state when the release was signed and may no longer be current.

File details

Details for the file operetta_compose-0.2.14-py3-none-any.whl.

File metadata

File hashes

Hashes for operetta_compose-0.2.14-py3-none-any.whl
Algorithm Hash digest
SHA256 07dc656c8987b38b3447625757421fbcffc1269a97fdd97a9224fd69835cfdf2
MD5 a057e794a1c34ad0ed9766482b131a56
BLAKE2b-256 2f5a24bd32e6ffb59b3e3d9c0e11523b16987a48d82c33b40fecd375cdf91457

See more details on using hashes here.

Provenance

The following attestation bundles were made for operetta_compose-0.2.14-py3-none-any.whl:

Publisher: build.yml on leukemia-kispi/operetta-compose

Attestations: Values shown here reflect the state when the release was signed and may no longer be current.

Supported by

AWS Cloud computing and Security Sponsor Datadog Monitoring Depot Continuous Integration Fastly CDN Google Download Analytics Pingdom Monitoring Sentry Error logging StatusPage Status page