plexora 0.0.30__tar.gz → 0.0.32__tar.gz

plexora-0.0.32/PKG-INFO

@@ -0,0 +1,249 @@
+Metadata-Version: 2.4
+Name: plexora
+Version: 0.0.32
+Summary: OpenSeadragon-based cellular image viewing and analysis tool.
+Author-email: BioCognia <support@biocognia.com>
+License-Expression: LicenseRef-Plexora-EULA-1.0
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Requires-Python: <3.15,>=3.12
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: aiohttp>=3.14.4
+Requires-Dist: anndata>=0.10
+Requires-Dist: biocognia<0.2,>=0.1.2
+Requires-Dist: Flask>=3.1
+Requires-Dist: fsspec>=2024.12
+Requires-Dist: h5py>=3.16.0
+Requires-Dist: hdf5plugin>=5
+Requires-Dist: imagecodecs
+Requires-Dist: itsdangerous>=2.2
+Requires-Dist: Jinja2>=3.1
+Requires-Dist: numba>=0.61
+Requires-Dist: numpy>=2.0
+Requires-Dist: ome-types>=0.6.3
+Requires-Dist: opencv-python-headless>=5.0.0.93
+Requires-Dist: openpyxl>=3.1
+Requires-Dist: onnxruntime<2,>=1.17
+Requires-Dist: orjson>=3.11
+Requires-Dist: pandas>=3.0.5
+Requires-Dist: Pillow>=13.0
+Requires-Dist: platformdirs>=4
+Requires-Dist: polars>=1.43
+Requires-Dist: pydantic<2.14,>=2.13
+Requires-Dist: reportlab>=5.0.1
+Requires-Dist: s3fs>=2024.12
+Requires-Dist: scikit-image
+Requires-Dist: scikit-learn>=1.9
+Requires-Dist: scipy
+Requires-Dist: shapely>=2.1.2
+Requires-Dist: spatialdata>=0.8.0
+Requires-Dist: spatialagents<0.3,>=0.2
+Requires-Dist: spatialbridge<0.3,>=0.2.1
+Requires-Dist: threadpoolctl>=3.6.0
+Requires-Dist: tifffile>=2026.7.31
+Requires-Dist: urllib3>=2.8.0
+Requires-Dist: waitress
+Requires-Dist: Werkzeug>=3.1.9
+Requires-Dist: zarr>=3
+Provides-Extra: jupyter
+Requires-Dist: ipython; extra == "jupyter"
+Requires-Dist: jupyter-server>=2.21; extra == "jupyter"
+Requires-Dist: jupyter-server-proxy; extra == "jupyter"
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytest-randomly>=4.1.0; extra == "dev"
+Requires-Dist: pytest-xdist>=3.6; extra == "dev"
+Requires-Dist: pytest-timeout>=2.3; extra == "dev"
+Provides-Extra: spatial
+Requires-Dist: pyarrow>=14; extra == "spatial"
+Provides-Extra: remote
+Requires-Dist: gcsfs>=2024.12; extra == "remote"
+Requires-Dist: adlfs>=2024.12; extra == "remote"
+Requires-Dist: wsidicom>=0.35; extra == "remote"
+Requires-Dist: pydicom>=3; extra == "remote"
+Requires-Dist: universal-pathlib>=0.2; extra == "remote"
+Provides-Extra: wsi
+Requires-Dist: openslide-python>=1.3; extra == "wsi"
+Requires-Dist: openslide-bin>=4.0; extra == "wsi"
+Requires-Dist: wsidicom>=0.35; extra == "wsi"
+Requires-Dist: pydicom>=3; extra == "wsi"
+Provides-Extra: ai
+Requires-Dist: mcp<3,>=2.2; extra == "ai"
+Requires-Dist: pyyaml>=6; extra == "ai"
+Provides-Extra: bridge
+Requires-Dist: spatialbridge[mcp]<0.3,>=0.2.1; extra == "bridge"
+Provides-Extra: volume3d
+Requires-Dist: torch>=2.5.1; extra == "volume3d"
+Requires-Dist: sam2>=1.1; extra == "volume3d"
+Provides-Extra: segment3d
+Requires-Dist: cellpose>=4; extra == "segment3d"
+Requires-Dist: torch>=2.5.1; extra == "segment3d"
+Provides-Extra: video
+Requires-Dist: imageio-ffmpeg>=0.5; extra == "video"
+Dynamic: license-file
+
+# Plexora
+
+![](./plexora/client/src/img/logo_with_text.svg)
+
+Plexora is a viewer for multiplexed imaging and spatial transcriptomics. It
+opens large images where they are, without converting or copying them, draws
+segmentation masks and cell tables over them, and runs on a laptop, in a
+notebook, on a remote workstation or on an HPC cluster.
+
+**Documentation: https://nirmallab.github.io/plexora/**
+
+![The Plexora viewer showing a multiplexed tissue image](./website/public/screenshots/home/viewer.webp)
+
+## Install
+
+```bash
+pip install plexora
+plexora
+```
+
+`plexora` starts the viewer and opens it in your browser. Python 3.12, 3.13 or
+3.14 is required. A desktop app for macOS, Windows and Linux is on the
+[releases page](https://github.com/nirmallab/plexora/releases). See
+[Installation](https://nirmallab.github.io/plexora/docs/getting-started/installation/).
+
+## Quick start
+
+In the app, choose **File → Import Sample…** and pick an image, a folder of
+files, or a Xenium or Visium run. From Python:
+
+```python
+import plexora
+
+name = plexora.import_sample("slide.ome.tif", "slide_mask.tif", "cells.csv", wait=True)
+plexora.view(name)   # in a notebook, shows the viewer inline
+```
+
+More in [Your first image](https://nirmallab.github.io/plexora/docs/getting-started/first-image/).
+
+## What it reads
+
+- Multiplexed images: OME-TIFF, TIFF, QPTIFF, OME-Zarr (local, `https://` or `s3://`)
+- Brightfield whole-slide images: SVS, NDPI, SCN, BIF, MRXS, DICOM
+- 10x Genomics Xenium, Visium and Visium HD output folders
+- SpatialData stores and AnnData tables; CSV, TSV and Parquet cell tables
+- Segmentation masks (label images) and cell boundary polygons
+
+The full list is in [Supported formats](https://nirmallab.github.io/plexora/docs/reference/supported-formats/).
+
+## Where to go next
+
+| I want to | Read |
+| --- | --- |
+| Use the viewer and its tools | [Image viewer](https://nirmallab.github.io/plexora/docs/features/viewer/), [Plugins](https://nirmallab.github.io/plexora/docs/plugins/) |
+| Script it from Python or a notebook | [Python](https://nirmallab.github.io/plexora/docs/python/), [Notebook](https://nirmallab.github.io/plexora/docs/notebook/) |
+| Look at data on a remote machine or cluster | [Remote and HPC](https://nirmallab.github.io/plexora/docs/features/remote/) |
+| Write a plugin | [Build a custom plugin](https://nirmallab.github.io/plexora/docs/plugins/build-a-plugin/) |
+| Look up a function or command | [Python API](https://nirmallab.github.io/plexora/docs/reference/python-api/), [Command line](https://nirmallab.github.io/plexora/docs/reference/cli/) |
+
+## Developing Plexora
+
+```bash
+git clone https://github.com/nirmallab/plexora.git
+cd plexora
+pip install -e ".[dev]"
+python -m pytest -q -p no:randomly
+```
+
+For the documentation site in `website/`, see [CONTRIBUTING_DOCS.md](./CONTRIBUTING_DOCS.md).
+Engineering notes live in [docs/internal/](./docs/internal/).
+
+## Usage data
+
+Plexora can send **anonymous usage counts** -- which features and plugins are
+used, how long tiles take to draw, which kinds of errors occur -- so we know
+what to improve. It never sends file, project, marker or gene names, cell
+data, coordinates, usernames, machine names, paths, prompts or anything typed
+into a tool; every field it may send is on an allowlist
+(`plexora/telemetry/schema.py`). Everything is queued on this machine first,
+nothing in Plexora waits for it, and it works air-gapped exactly as before.
+
+It is on by default and a notice says so the first time. Any one of these turns
+it off:
+
+```bash
+plexora telemetry off        # or: Settings > Usage data
+export DO_NOT_TRACK=1        # honoured everywhere
+export PLEXORA_TELEMETRY=off
+```
+
+`plexora telemetry preview` prints exactly what the next upload would contain,
+and `plexora telemetry status` says which of the above is in force.
+[docs/TELEMETRY.md](./docs/TELEMETRY.md) has the details.
+
+## Free and Pro
+
+**Free** is everything described above: every image, table and modality, every
+tool's manual features, remote, HPC and notebook viewing, and export. It needs no
+account, no activation and no network, it never asks, and anyone may use it for
+any purpose, commercial work included.
+
+**Pro** adds Plexora AI (guided gating and QC sessions an agent runs with you,
+the evidence and analysis tools it uses, and the chat), Plexora 3D (analysing
+z-stacks and time series beyond viewing them), spatial transcriptomics
+(Xenium, Visium and Visium HD) and Video Studio (videos made from the viewer).
+A 30-day trial is everything in Pro. External MCP access, for an outside coding
+agent, is off by default and not part of Pro; an administrator can turn it on
+for a licence. Pro is a yearly subscription per seat, at an academic or a
+commercial price, and both are bought online from the
+[pricing page](https://biocognia.com/#pricing): one seat is an
+individual account, two or more make a team. Licences, devices and AI credits
+are managed on the BioCognia platform, which Plexora shares with SCIMAP Pro: you
+sign in at [account.biocognia.com](https://account.biocognia.com), never in
+Plexora. In Settings > Account, **Connect this device** shows a short code and
+opens the page to approve it; or, from a terminal:
+
+```bash
+plexora license status
+plexora license activate                            # this computer: prints a code to approve in the browser
+plexora license activate BIOC-XXXX-XXXX-XXXX-XXXX   # with your licence key from the portal, no browser needed
+plexora license activate --cluster --name O2        # a whole HPC cluster, once, from a login node
+plexora license install lab.bioc                    # an offline licence file
+plexora license trial                               # 30 days of Pro
+```
+
+A licence check sends the licence certificate and a hash that identifies the
+device. It never sends your data, file names, machine names or anything
+about what you are looking at. When a licence ends, everything Free keeps
+working, and every gate, ROI, figure and export you made, with or without AI,
+stays yours and editable. AI model providers your agent uses bill you
+separately. [docs/LICENSING.md](./docs/LICENSING.md) has the details.
+
+## License
+
+Plexora is licensed by BioCognia under the **Plexora End User Licence Agreement
+1.0** (`LicenseRef-Plexora-EULA-1.0`, see [LICENSE](./LICENSE)). It is **not** an
+open source license. In short:
+
+| | |
+|---|---|
+| Plexora Free, for any purpose: research, teaching, personal or commercial | ✅ Free, no account or licence key |
+| Plexora Pro for academic research and teaching | Per seat, per year, at the academic price |
+| Plexora Pro for commercial use | Per seat, per year, at the commercial price |
+| Redistributing Plexora unmodified, with the licence attached | ✅ Allowed |
+| Patching your own copy to fix a bug or a compatibility problem | ✅ Allowed |
+| Publishing a fork, a patched build, or a renamed version | ❌ Not allowed |
+
+Prices, and Buy for either use class, are on the
+[pricing page](https://biocognia.com/#pricing); a subscription
+renews at the price it was bought at.
+
+**Plugins are a deliberate exception.** Anything you build against the documented
+extension interfaces — the `plexora.plugins` entry point group and the `plexora.api`
+package — is yours. You may distribute and sell your plugin under whatever license
+you like, and you do not need our permission. Extending Plexora through the plugin
+API is the supported way to change what it does; editing its source is not.
+
+For licensing questions, contact support@biocognia.com.
+
+Some bundled components carry their own licenses, which are unaffected by the above —
+see section 13 of [LICENSE](./LICENSE).

plexora-0.0.32/README.md

@@ -0,0 +1,161 @@
+# Plexora
+
+![](./plexora/client/src/img/logo_with_text.svg)
+
+Plexora is a viewer for multiplexed imaging and spatial transcriptomics. It
+opens large images where they are, without converting or copying them, draws
+segmentation masks and cell tables over them, and runs on a laptop, in a
+notebook, on a remote workstation or on an HPC cluster.
+
+**Documentation: https://nirmallab.github.io/plexora/**
+
+![The Plexora viewer showing a multiplexed tissue image](./website/public/screenshots/home/viewer.webp)
+
+## Install
+
+```bash
+pip install plexora
+plexora
+```
+
+`plexora` starts the viewer and opens it in your browser. Python 3.12, 3.13 or
+3.14 is required. A desktop app for macOS, Windows and Linux is on the
+[releases page](https://github.com/nirmallab/plexora/releases). See
+[Installation](https://nirmallab.github.io/plexora/docs/getting-started/installation/).
+
+## Quick start
+
+In the app, choose **File → Import Sample…** and pick an image, a folder of
+files, or a Xenium or Visium run. From Python:
+
+```python
+import plexora
+
+name = plexora.import_sample("slide.ome.tif", "slide_mask.tif", "cells.csv", wait=True)
+plexora.view(name)   # in a notebook, shows the viewer inline
+```
+
+More in [Your first image](https://nirmallab.github.io/plexora/docs/getting-started/first-image/).
+
+## What it reads
+
+- Multiplexed images: OME-TIFF, TIFF, QPTIFF, OME-Zarr (local, `https://` or `s3://`)
+- Brightfield whole-slide images: SVS, NDPI, SCN, BIF, MRXS, DICOM
+- 10x Genomics Xenium, Visium and Visium HD output folders
+- SpatialData stores and AnnData tables; CSV, TSV and Parquet cell tables
+- Segmentation masks (label images) and cell boundary polygons
+
+The full list is in [Supported formats](https://nirmallab.github.io/plexora/docs/reference/supported-formats/).
+
+## Where to go next
+
+| I want to | Read |
+| --- | --- |
+| Use the viewer and its tools | [Image viewer](https://nirmallab.github.io/plexora/docs/features/viewer/), [Plugins](https://nirmallab.github.io/plexora/docs/plugins/) |
+| Script it from Python or a notebook | [Python](https://nirmallab.github.io/plexora/docs/python/), [Notebook](https://nirmallab.github.io/plexora/docs/notebook/) |
+| Look at data on a remote machine or cluster | [Remote and HPC](https://nirmallab.github.io/plexora/docs/features/remote/) |
+| Write a plugin | [Build a custom plugin](https://nirmallab.github.io/plexora/docs/plugins/build-a-plugin/) |
+| Look up a function or command | [Python API](https://nirmallab.github.io/plexora/docs/reference/python-api/), [Command line](https://nirmallab.github.io/plexora/docs/reference/cli/) |
+
+## Developing Plexora
+
+```bash
+git clone https://github.com/nirmallab/plexora.git
+cd plexora
+pip install -e ".[dev]"
+python -m pytest -q -p no:randomly
+```
+
+For the documentation site in `website/`, see [CONTRIBUTING_DOCS.md](./CONTRIBUTING_DOCS.md).
+Engineering notes live in [docs/internal/](./docs/internal/).
+
+## Usage data
+
+Plexora can send **anonymous usage counts** -- which features and plugins are
+used, how long tiles take to draw, which kinds of errors occur -- so we know
+what to improve. It never sends file, project, marker or gene names, cell
+data, coordinates, usernames, machine names, paths, prompts or anything typed
+into a tool; every field it may send is on an allowlist
+(`plexora/telemetry/schema.py`). Everything is queued on this machine first,
+nothing in Plexora waits for it, and it works air-gapped exactly as before.
+
+It is on by default and a notice says so the first time. Any one of these turns
+it off:
+
+```bash
+plexora telemetry off        # or: Settings > Usage data
+export DO_NOT_TRACK=1        # honoured everywhere
+export PLEXORA_TELEMETRY=off
+```
+
+`plexora telemetry preview` prints exactly what the next upload would contain,
+and `plexora telemetry status` says which of the above is in force.
+[docs/TELEMETRY.md](./docs/TELEMETRY.md) has the details.
+
+## Free and Pro
+
+**Free** is everything described above: every image, table and modality, every
+tool's manual features, remote, HPC and notebook viewing, and export. It needs no
+account, no activation and no network, it never asks, and anyone may use it for
+any purpose, commercial work included.
+
+**Pro** adds Plexora AI (guided gating and QC sessions an agent runs with you,
+the evidence and analysis tools it uses, and the chat), Plexora 3D (analysing
+z-stacks and time series beyond viewing them), spatial transcriptomics
+(Xenium, Visium and Visium HD) and Video Studio (videos made from the viewer).
+A 30-day trial is everything in Pro. External MCP access, for an outside coding
+agent, is off by default and not part of Pro; an administrator can turn it on
+for a licence. Pro is a yearly subscription per seat, at an academic or a
+commercial price, and both are bought online from the
+[pricing page](https://biocognia.com/#pricing): one seat is an
+individual account, two or more make a team. Licences, devices and AI credits
+are managed on the BioCognia platform, which Plexora shares with SCIMAP Pro: you
+sign in at [account.biocognia.com](https://account.biocognia.com), never in
+Plexora. In Settings > Account, **Connect this device** shows a short code and
+opens the page to approve it; or, from a terminal:
+
+```bash
+plexora license status
+plexora license activate                            # this computer: prints a code to approve in the browser
+plexora license activate BIOC-XXXX-XXXX-XXXX-XXXX   # with your licence key from the portal, no browser needed
+plexora license activate --cluster --name O2        # a whole HPC cluster, once, from a login node
+plexora license install lab.bioc                    # an offline licence file
+plexora license trial                               # 30 days of Pro
+```
+
+A licence check sends the licence certificate and a hash that identifies the
+device. It never sends your data, file names, machine names or anything
+about what you are looking at. When a licence ends, everything Free keeps
+working, and every gate, ROI, figure and export you made, with or without AI,
+stays yours and editable. AI model providers your agent uses bill you
+separately. [docs/LICENSING.md](./docs/LICENSING.md) has the details.
+
+## License
+
+Plexora is licensed by BioCognia under the **Plexora End User Licence Agreement
+1.0** (`LicenseRef-Plexora-EULA-1.0`, see [LICENSE](./LICENSE)). It is **not** an
+open source license. In short:
+
+| | |
+|---|---|
+| Plexora Free, for any purpose: research, teaching, personal or commercial | ✅ Free, no account or licence key |
+| Plexora Pro for academic research and teaching | Per seat, per year, at the academic price |
+| Plexora Pro for commercial use | Per seat, per year, at the commercial price |
+| Redistributing Plexora unmodified, with the licence attached | ✅ Allowed |
+| Patching your own copy to fix a bug or a compatibility problem | ✅ Allowed |
+| Publishing a fork, a patched build, or a renamed version | ❌ Not allowed |
+
+Prices, and Buy for either use class, are on the
+[pricing page](https://biocognia.com/#pricing); a subscription
+renews at the price it was bought at.
+
+**Plugins are a deliberate exception.** Anything you build against the documented
+extension interfaces — the `plexora.plugins` entry point group and the `plexora.api`
+package — is yours. You may distribute and sell your plugin under whatever license
+you like, and you do not need our permission. Extending Plexora through the plugin
+API is the supported way to change what it does; editing its source is not.
+
+For licensing questions, contact support@biocognia.com.
+
+Some bundled components carry their own licenses, which are unaffected by the above —
+see section 13 of [LICENSE](./LICENSE).