ashlarUC2 1.18.1__tar.gz

ashlaruc2-1.18.1/LICENSE

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+MIT License
+
+Copyright (c) 2022 President and Fellows of Harvard College
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

ashlaruc2-1.18.1/MANIFEST.in

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+include versioneer.py
+include ashlarUC2/_version.py
+recursive-include ashlarUC2/jars *.jar

ashlaruc2-1.18.1/PKG-INFO

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+Metadata-Version: 2.1
+Name: ashlarUC2
+Version: 1.18.1
+Summary: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration
+Home-page: https://github.com/openuc2/ashlar
+Download-URL: https://github.com/openuc2/ashlar/archive/v1.18.1.tar.gz
+Author: Jeremy Muhlich modified by Benedict Diederich
+Author-email: benedictdied@gmail.com
+License: MIT License
+Keywords: scripts,microscopy,registration,stitching
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: End Users/Desktop
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Natural Language :: English
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+Requires-Dist: numpy>=1.18.1
+Requires-Dist: pyjnius>=1.2.1
+Requires-Dist: matplotlib>=3.1.2
+Requires-Dist: networkx>=2.4
+Requires-Dist: scipy>=1.4.1
+Requires-Dist: scikit-image<0.20,>=0.19.2
+Requires-Dist: scikit-learn>=0.21.1
+Requires-Dist: tifffile>=2023.3.15
+Requires-Dist: zarr>=2.11.3
+Requires-Dist: blessed>=1.17
+
+
+
+ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration
+
+Ashlar implements efficient combined stitching and registration of multi-channel
+image mosaics collected using the Tissue-CycIF microscopy protocol [1]_. Although
+originally developed for CycIF, it may also be applicable to other tiled and/or
+cyclic imaging approaches. The package offers both a command line script for the
+most common use cases as well as an API for building more specialized tools.
+
+.. [1] Tissue-CycIF is multi-round immunofluorescence microscopy on large fixed
+   tissue samples. See https://doi.org/10.1101/151738 for details.
+

ashlaruc2-1.18.1/README.md

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+**ATTENTION:** This is a modified version used by UC2 and mirrored by PyPi to make it installable for ImSwitch. 
+
+# ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration
+
+## Whole-slide microscopy image stitching and registration in Python
+
+**Ashlar** performs fast, high-quality stitching of microscopy images. It also
+co-registers multiple rounds of cyclic imaging for methods such as CyCIF and
+CODEX. Ashlar can read image data directly from BioFormats-supported microscope
+vendor file formats as well as a directory of plain TIFF files. Output is saved
+as pyramidal, tiled OME-TIFF.
+
+Note that Ashlar requires unstitched individual "tile" images as input, so it is
+not suitable for microscopes or slide scanners that only provide pre-stitched
+images.
+
+**Visit [labsyspharm.github.io/ashlar/](https://labsyspharm.github.io/ashlar/) for the most up-to-date information on ASHLAR.**
+
+## Usage
+
+```
+ashlar [-h] [-o PATH] [-c CHANNEL] [--flip-x] [--flip-y]
+       [--flip-mosaic-x] [--flip-mosaic-y]
+       [--output-channels CHANNEL [CHANNEL ...]] [-m SHIFT]
+       [--stitch-alpha ALPHA] [--filter-sigma SIGMA]
+       [--tile-size PIXELS] [--ffp FILE [FILE ...]]
+       [--dfp FILE [FILE ...]] [--plates] [-q] [--version]
+       FILE [FILE ...]
+
+Stitch and align multi-tile cyclic microscope images
+
+positional arguments:
+  FILE                  Image file(s) to be processed, one per cycle
+
+optional arguments:
+  -h, --help            Show this help message and exit
+  -o PATH, --output PATH
+                        Output file. If PATH ends in .ome.tif a pyramidal OME-
+                        TIFF will be written. If PATH ends in just .tif and
+                        includes {cycle} and {channel} placeholders, a series
+                        of single-channel plain TIFF files will be written. If
+                        PATH starts with a relative or absolute path to
+                        another directory, that directory must already exist.
+                        (default: ashlar_output.ome.tif)
+  -c CHANNEL, --align-channel CHANNEL
+                        Reference channel number for image alignment.
+                        Numbering starts at 0. (default: 0)
+  --flip-x              Flip tile positions left-to-right
+  --flip-y              Flip tile positions top-to-bottom
+  --flip-mosaic-x       Flip output image left-to-right
+  --flip-mosaic-y       Flip output image top-to-bottom
+  --output-channels CHANNEL [CHANNEL ...]
+                        Output only specified channels for each cycle.
+                        Numbering starts at 0. (default: all channels)
+  -m SHIFT, --maximum-shift SHIFT
+                        Maximum allowed per-tile corrective shift in microns
+                        (default: 15)
+  --stitch-alpha ALPHA  Significance level for permutation testing during
+                        alignment error quantification. Larger values include
+                        more tile pairs in the spanning tree at the cost of
+                        increased false positives. (default: 0.01)
+  --filter-sigma SIGMA  Filter images before alignment using a Gaussian kernel
+                        with s.d. of SIGMA pixels (default: no filtering)
+  --tile-size PIXELS    Pyramid tile size for OME-TIFF output (default: 1024)
+  --ffp FILE [FILE ...]
+                        Perform flat field illumination correction using the
+                        given profile image. Specify one common file for all
+                        cycles or one file for every cycle. Channel counts
+                        must match input files. (default: no flat field
+                        correction)
+  --dfp FILE [FILE ...]
+                        Perform dark field illumination correction using the
+                        given profile image. Specify one common file for all
+                        cycles or one file for every cycle. Channel counts
+                        must match input files. (default: no dark field
+                        correction)
+  --plates              Enable plate mode for HTS data
+  -q, --quiet           Suppress progress display
+  --version             Show program's version number and exit
+```
+
+## Installation
+
+### Pip install
+
+Ashlar can be installed in most Python environments using `pip`:
+``` bash
+pip install ashlar
+```
+
+### Using a conda environment
+
+If you don't already have [miniconda](https://docs.conda.io/en/latest/miniconda.html)
+or [Anaconda](https://www.anaconda.com/products/individual), download the python
+3.x version and install. Then, run the following commands from a terminal (Linux/Mac)
+or command prompt (Windows):
+
+Create a named conda environment with python 3.10:
+```bash
+conda create -y -n ashlar python=3.10
+```
+
+Activate the conda environment:
+```bash
+conda activate ashlar
+```
+
+In the activated environment, install dependencies and ashlar itself:
+```bash
+conda install -y -c conda-forge numpy scipy matplotlib networkx scikit-image=0.19 scikit-learn "tifffile>=2023.3.15" zarr pyjnius blessed
+pip install ashlar
+```
+
+### Docker image
+
+The docker image of ashlar is on DockerHub at `labsyspharm/ashlar` which should be
+suitable for many use cases.

ashlaruc2-1.18.1/ashlarUC2/__init__.py

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+# Versioneer boilerplate.
+__version__ = "1.18.1"
+
+# Import all the things.
+from . import *