piximi-beta

https://github.com/piximi/piximi-beta

Science Score: 44.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
○
DOI references
○
Academic publication links
○
Academic email domains
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (11.3%) to scientific vocabulary

Last synced: 10 months ago · JSON representation ·

Repository

Basic Info

Host: GitHub
Owner: piximi
License: other
Language: TypeScript
Default Branch: master
Homepage: https://piximi.github.io/piximi-beta
Size: 371 MB

Statistics

Stars: 0
Watchers: 3
Forks: 0
Open Issues: 0
Releases: 0

Created over 2 years ago · Last pushed almost 2 years ago

Metadata Files

Readme License Citation

Piximi is a free, open source web app for performing image understanding tasks. It’s written by dozens of engineers and scientists from institutions like the Biological Research Centre Szeged, Broad Institute of MIT and Harvard, Chan Zuckerberg Initiative, ETH Zurich, and FIMM Helsinki.

Piximi's target users are computational or non-computational scientists interested in image analysis from fields like astronomy, biology, and medicine.

Try Piximi now at Piximi.app!

Development

Available Scripts

In the project directory, you can run:

`yarn install && yarn prepare`

Install all project dependencies.

`yarn start`

Runs the app in the development mode.
Open http://localhost:3000 to view it in the browser.

`yarn build`

Builds the app for production to the build folder.

`yarn test`

Runs the tests. Note that for tests using tensorflow you need to specify the custom environment:

yarn test --env=./src/utils/common/models/utils/custom-test-env.js

Docker

To run as a docker container, clone the repo, build the image and run it:

git clone https://github.com/piximi/piximi docker build -t <image_name> piximi/ docker run -p 3000:3000 --name <container_name> <image_name>

If you encounter the following message: The build failed because the process exited too early. This probably means the system ran out of memory or someone calledkill -9on the process. and you are running Docker Desktop, you will need to increase memory resources. 8GB memory should be sufficient.

Alternatively, download the pre-built image and run it directly from Docker Hub:

docker run -p 3000:3000 --name piximi gnodar01/piximi:0.1.0

Owner

Name: Piximi
Login: piximi
Kind: organization

Website: www.piximi.app
Repositories: 20
Profile: https://github.com/piximi

a free, open-source web-based image understanding app

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Goodman"
  given-names: "Allen"
  orcid: "https://orcid.org/0000-0002-6434-2320"
- family-names: "Lucas"
  given-names: "Alice"
  orcid: "https://orcid.org/0000-0001-5914-4154"
- family-names: "Gogoberidze"
  given-names: "Nodar"
  orcid: "https://orcid.org/0000-0002-9395-4676"
- family-names: "Moser"
  given-names: "Levin"
  orcid: "https://orcid.org/0000-0002-4212-404X"
- family-names: "Dao"
  given-names: "David"
  orcid: "https://orcid.org/0000-0002-6752-9166"
- family-names: "Friedrich"
  given-names: "Christoph"
- family-names: "Paavolainen"
  given-names: "Lassi"
  orcid: "https://orcid.org/0000-0003-1508-2718"
- family-names: "Papaleo"
  given-names: "Andréa"
  orcid: "https://orcid.org/0000-0003-2269-9337"
- family-names: "Stirling"
  given-names: "David"
  orcid: "https://orcid.org/0000-0001-6802-4103"
- family-names: "Hubis"
  given-names: "Frances"
- family-names: "Molnar"
  given-names: "Csaba"
  orcid: "https://orcid.org/0000-0002-6124-1209"
- family-names: "Ryder"
  given-names: "Pearl"
  orcid: "https://orcid.org/0000-0003-3699-3633"
- family-names: "Wang"
  given-names: "Rex"
- family-names: "Hung"
  given-names: "Jane"
- family-names: "Horvath"
  given-names: "Peter"
  orcid: "https://orcid.org/0000-0002-4492-1798"
- family-names: "Cimini"
  given-names: "Beth"
  orcid: "https://orcid.org/0000-0001-9640-9318"
- family-names: "Carpenter"
  given-names: "Anne"
  orcid: "https://orcid.org/0000-0003-1555-8261"
title: "Piximi - an images to discovery web platform"
version: 0.0.0
date-released: 2021-06-29
url: "https://github.com/piximi/piximi"

GitHub Events

Total

Last Year

Dependencies

.github/workflows/deploy.yml actions

actions/checkout v2 composite
actions/setup-node v2 composite
peaceiris/actions-gh-pages v3 composite

.github/workflows/test.yml actions

actions/checkout v2 composite
actions/setup-node v2 composite

Dockerfile docker

node 16.13-bullseye-slim build

package.json npm

@storybook/addon-essentials ^7.0.26 development
@storybook/addon-interactions ^7.0.26 development
@storybook/addon-links ^7.0.26 development
@storybook/addon-styling ^1.3.2 development
@storybook/blocks ^7.0.26 development
@storybook/preset-create-react-app ^7.0.26 development
@storybook/react ^7.0.26 development
@storybook/react-webpack5 ^7.0.26 development
@storybook/testing-library ^0.0.14-next.2 development
@tensorflow/tfjs-node 4.2.0 development
babel-plugin-named-exports-order ^0.0.2 development
canvas ^2.9.1 development
eslint-plugin-storybook ^0.6.12 development
husky ^8.0.0 development
jest-canvas-mock ^2.3.0 development
lint-staged ^13.1.0 development
prettier ^2.2.1 development
prop-types ^15.8.1 development
react-test-renderer ^18.2.0 development
storybook ^7.0.26 development
ts-node ^10.9.1 development
ts-prune ^0.10.3 development
tslib ^2.4.0 development
webpack ^5.74.0 development
@clarketm/saga-monitor ^2.0.1
@emotion/react ^11.6.0
@emotion/styled ^11.6.0
@fontsource/material-icons ^5.0.5
@fontsource/roboto ^5.0.5
@mui/icons-material ^5.1.1
@mui/lab ^5.0.0-alpha.51
@mui/material ^5.1.1
@mui/styles ^5.1.1
@nivo/core ^0.79.0
@nivo/heatmap ^0.79.1
@nivo/legends ^0.79.1
@nivo/line ^0.79.1
@react-hook/resize-observer ^1.2.4
@reduxjs/toolkit ^1.5.0
@sentry/react ^6.15.0
@tensorflow/tfjs 4.2.0
@testing-library/dom ^7.21.4
@testing-library/jest-dom ^5.15.0
@testing-library/react ^11.2.2
@testing-library/user-event ^12.8.3
@types/file-saver ^2.0.4
@types/jest ^27.5.1
@types/lodash ^4.14.177
@types/node ^18.7.18
@types/numeral ^2.0.2
@types/react ^17.0.39
@types/react-color ^3.0.4
@types/react-dom ^17.0.11
@types/react-redux ^7.1.13
@types/react-vis ^1.11.10
@types/redux-logger ^3.0.8
@types/uuid ^8.3.3
dicom-parser ^1.8.13
dicom.ts ^1.0.5
file-saver ^2.0.5
fp-ts ^2.13.1
i18next 19.0.0
image-js 0.35.2
imjoy-rpc 0.5.21
io-ts ^2.2.20
jszip ^3.7.1
konva ^8.3.0
lodash ^4.17.20
ngraph.graph ^19.1.0
ngraph.path ^1.3.1
numeral ^2.0.6
react ^17.0.2
react-color ^2.19.3
react-dnd ^15.0.0
react-dnd-html5-backend ^15.0.0
react-dom ^17.0.2
react-error-boundary ^3.1.4
react-i18next ^11.13.0
react-konva ^17.0.1-3
react-redux ^7.2.2
react-router-dom 6.4.0
react-scripts 5.0.0
redux-logger ^3.0.6
redux-saga ^1.1.3
semver ^7.5.4
stacktrace-js ^2.0.2
ts-priority-queue ^0.1.1
typescript ^4.5.2
use-dropbox-chooser ^0.0.5
use-image ^1.0.7
use-sound ^4.0.1
uuid ^8.3.2
web-vitals ^2.1.2
zarr ^0.6.1

yarn.lock npm

2146 dependencies

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science