celldetective 1.2.2__py3-none-any.whl → 1.2.2.post2__py3-none-any.whl

celldetective/models/segmentation_effectors/primNK_cfse/config_input.json

@@ -1,29 +0,0 @@
-{
-    "channels": [
-        "effector_fluo_channel",
-        "None"
-    ],
-    "diameter": 30.0,
-    "cellprob_threshold": 0.0,
-    "flow_threshold": 0.4,
-    "normalization_percentile": [
-        true,
-        true
-    ],
-    "normalization_clip": [
-        true,
-        true
-    ],
-    "normalization_values": [
-        [
-            0.5,
-            99.0
-        ],
-        [
-            1.0,
-            99.0
-        ]
-    ],
-    "model_type": "cellpose",
-    "spatial_calibration": 0.21783999999999998
-}

celldetective/models/segmentation_effectors/primNK_cfse/training_instructions.json

@@ -1,37 +0,0 @@
-{
-    "model_name": "cp-cfse-transfer",
-    "model_type": "cellpose",
-    "pretrained": "/home/limozin/Documents/GitHub/celldetective/celldetective/models/segmentation_generic/CP_cyto2",
-    "spatial_calibration": 0.21783999999999998,
-    "channel_option": [
-        "effector_fluo_channel",
-        "None"
-    ],
-    "normalization_percentile": [
-        true,
-        true
-    ],
-    "normalization_clip": [
-        true,
-        true
-    ],
-    "normalization_values": [
-        [
-            0.5,
-            99.0
-        ],
-        [
-            1.0,
-            99.0
-        ]
-    ],
-    "ds": [
-        "/home/limozin/Desktop/primNK_w_MCF7/dataset"
-    ],
-    "augmentation_factor": 1.5,
-    "validation_split": 0.2,
-    "learning_rate": 0.001,
-    "batch_size": 8,
-    "epochs": 3000,
-    "target_directory": "/home/limozin/Documents/GitHub/celldetective/celldetective/models/segmentation_effectors"
-}

celldetective/models/segmentation_effectors/ricm-bimodal/config_input.json

@@ -1,130 +0,0 @@
-{
-    "channels": [
-        "adhesion_channel",
-        "brightfield_channel"
-    ],
-    "diameter": 30.0,
-    "cellprob_threshold": 0.0,
-    "flow_threshold": 0.4,
-    "normalization_percentile": [
-        false,
-        true
-    ],
-    "normalization_clip": [
-        true,
-        true
-    ],
-    "normalization_values": [
-        [
-            0.75,
-            1.25
-        ],
-        [
-            1.0,
-            99.0
-        ]
-    ],
-    "model_type": "cellpose",
-    "spatial_calibration": 0.2,
-    "dataset": {
-        "train": [
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Marie_100_0109.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/StaticRICM-Dom-20191016-Her2-10nM-C7b21_200_0057.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/StaticRICM-Dom-20191016-Her2-10nM-C7b21_200_0058.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/AdhesionDalia-26-08_209_0022.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/AdhesionDalia-26-08_2015_0039.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Exp20190619_700_0024.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia-2021-04-27_C7b21NF-incub-with-cells-test_605_0037.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia08052020_102_0039.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_200_0034.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia08052020_103_0011.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Marie_701_0004.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_201_0035.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia08052020_100_0016.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia-2021-04-27_C7b21NF-incub-with-cells-test_202_0020.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dominique20191016_303_0016.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Marie_502_0000.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/20231213_RICM_2C11_PP2_normed_201_0000.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia08052020_105_0031.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/AdhesionDalia-26-08_2012_0039.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia-2021-04-27_C7b21NF-incub-with-cells-test_608_0028.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_2012_0027.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia08052020_101_0021.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia-2021-04-27_C7b21NF-incub-with-cells-test_302_0039.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia08052020_104_0036.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Marie_801_0036.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_502_0036.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Marie_808_0173.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_5011_0006.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/StaticRICM-Dom-20191016-Her2-10nM-C7b21_800_0019.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dominique20191016_302_0039.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Exp20190619_400_0061.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/20231213_RICM_2C11_PP2_normed_106_0117.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_402_0039.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/20231213_RICM_2C11_PP2_normed_305_0158.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/20231213_RICM_2C11_PP2_normed_308_0191.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/StaticRICM-Dom-20191016-Her2-10nM-C7b21_800_0050.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Marie_500_0127.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/20231213_RICM_2C11_PP2_normed_300_0009.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Marie_701_0082.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/StaticRICM-Dom-20191016-Her2-10nM-C7b21_800_0000.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_303_0019.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/StaticRICM-Dom-20191016-Her2-10nM-C7b21_800_0002.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Exp20190619_700_0009.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Marie_701_0055.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia08052020_104_0019.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/20231213_RICM_2C11_PP2_normed_600_0108.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/StaticRICM-Dom-20191016-Her2-10nM-C7b21_800_0021.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/20231213_RICM_2C11_PP2_normed_600_0193_roi_491_996_143_708.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/20231213_RICM_2C11_PP2_normed_106_0000.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_2014_0038.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia-2021-04-27_C7b21NF-incub-with-cells-test_604_0033.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_303_0025.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia08052020_105_0038.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia-2021-04-27_C7b21NF-incub-with-cells-test_201_0039.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/20231213_RICM_2C11_PP2_normed_406_0202.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia08052020_105_0028.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Marie_600_0172.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/20231213_RICM_2C11_PP2_normed_600_0193.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_3011_0036.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_203_0024.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_209_0020.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/20231213_RICM_2C11_PP2_normed_100_0181.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_201_0034.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_704_0010.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_2014_0034.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_303_0021.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Exp20190619_700_0023.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Marie_600_0019.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Marie_808_0016.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dominique20191016_303_0039.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia08052020_103_0034.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia08052020_101_0038.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Marie_100_0007.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia-2021-04-27_C7b21NF-incub-with-cells-test_607_0035.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Marie_200_0006.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_206_0030.tif"
-        ],
-        "validation": [
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia-2021-04-27_C7b21NF-incub-with-cells-test_6011_0026.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia08052020_100_0035.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/AdhesionDalia-26-08_208_0020.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia08052020_102_0031.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia-2021-04-27_C7b21NF-incub-with-cells-test_200_0039.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Marie_502_0150.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dominique20191016_304_0033.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia08052020_1015_0036.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/StaticRICM-Dom-20191016-Her2-10nM-C7b21_200_0061.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_5013_0000.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Exp20190619_700_0025.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia08052020_105_0039.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Marie_801_0177.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_504_0016.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dominique20191016_301_0039.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia01092020_504_0037.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dominique20191016_305_0030.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/Dalia-2021-04-27_C7b21NF-incub-with-cells-test_606_0036.tif",
-            "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined/20231213_RICM_2C11_PP2_normed_300_0087.tif"
-        ]
-    }
-}

celldetective/models/segmentation_effectors/ricm-bimodal/training_instructions.json

@@ -1,37 +0,0 @@
-{
-    "model_name": "ricm-bimodal",
-    "model_type": "cellpose",
-    "pretrained": null,
-    "spatial_calibration": 0.2,
-    "channel_option": [
-        "adhesion_channel",
-        "brightfield_channel"
-    ],
-    "normalization_percentile": [
-        false,
-        true
-    ],
-    "normalization_clip": [
-        true,
-        true
-    ],
-    "normalization_values": [
-        [
-            0.75,
-            1.25
-        ],
-        [
-            1.0,
-            99.0
-        ]
-    ],
-    "ds": [
-        "/home/kheya/Documents/torro-cinam/DATASET-RICM/combined"
-    ],
-    "augmentation_factor": 3.0,
-    "validation_split": 0.2,
-    "learning_rate": 0.008,
-    "batch_size": 16,
-    "epochs": 3000,
-    "target_directory": "/home/kheya/Documents/torro-cinam/GitHub/celldetective/celldetective/models/segmentation_effectors"
-}

celldetective-1.2.2.dist-info/METADATA

@@ -1,312 +0,0 @@
-Metadata-Version: 2.1
-Name: celldetective
-Version: 1.2.2
-Summary: description
-Home-page: http://github.com/remyeltorro/celldetective
-Author: Rémy Torro
-Author-email: remy.torro@inserm.fr
-License: GPL-3.0
-Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: wheel
-Requires-Dist: nbsphinx
-Requires-Dist: nbsphinx-link
-Requires-Dist: sphinx-rtd-theme
-Requires-Dist: sphinx
-Requires-Dist: jinja2
-Requires-Dist: ipykernel
-Requires-Dist: stardist
-Requires-Dist: cellpose<3
-Requires-Dist: scikit-learn
-Requires-Dist: btrack
-Requires-Dist: tensorflow~=2.15.0
-Requires-Dist: napari
-Requires-Dist: tqdm
-Requires-Dist: mahotas
-Requires-Dist: fonticon-materialdesignicons6
-Requires-Dist: art
-Requires-Dist: lifelines
-Requires-Dist: setuptools
-Requires-Dist: scipy
-Requires-Dist: seaborn
-Requires-Dist: opencv-python-headless==4.7.0.72
-Requires-Dist: liblapack
-Requires-Dist: gputools
-Requires-Dist: lmfit
-Requires-Dist: superqt[cmap]
-Requires-Dist: matplotlib-scalebar
-Requires-Dist: numpy==1.26.4
-
-# Celldetective
-
-<embed>
-    <p align="center">
-    <img src="https://github.com/remyeltorro/celldetective/blob/main/celldetective/icons/logo-large.png" width="33%" />
-    </p>
-</embed>
-
-![ico1](https://img.shields.io/readthedocs/celldetective?link=https%3A%2F%2Fcelldetective.readthedocs.io%2Fen%2Flatest%2Findex.html)
-![ico17](https://github.com/remyeltorro/celldetective/actions/workflows/test.yml/badge.svg)
-![ico4](https://img.shields.io/pypi/v/celldetective)
-![ico6](https://img.shields.io/github/downloads/remyeltorro/celldetective/total)
-![ico5](https://img.shields.io/pypi/dm/celldetective)
-![ico2](https://img.shields.io/github/forks/remyeltorro/celldetective?link=https%3A%2F%2Fgithub.com%2Fremyeltorro%2Fcelldetective%2Fforks)
-![ico3](https://img.shields.io/github/stars/remyeltorro/celldetective?link=https%3A%2F%2Fgithub.com%2Fremyeltorro%2Fcelldetective%2Fstargazers)
-
-Celldetective is a python package and software to perform single-cell
-analysis on multimodal time lapse microscopy images.
-
--   **Documentation:** <https://celldetective.readthedocs.io>
--   **Source code:** <https://github.com/remyeltorro/celldetective>
--   **Bug reports:**
-    <https://github.com/remyeltorro/celldetective/issues/new/choose>
--   **Datasets, models and demos:**
-    <https://zenodo.org/records/10650279>
-
-## Overview
-
-<embed>
-    <p align="center">
-    <img src="https://github.com/remyeltorro/celldetective/blob/main/docs/source/_static/celldetective-blocks.png" width="90%" />
-    </p>
-</embed>
-
-Despite notable efforts in the development of user-friendly softwares
-that integrate state-of-the-art solutions to perform single cell
-analysis, very few are designed for time-lapse data and even less for
-multimodal problems where cells populations are mixed and can only be
-separated through the use of multimodal information. Few software
-solutions provide, to our knowledge, the extraction of response
-functions from single cell events such as the dynamic survival of a
-population directly in the GUI, as coding skills are usually required to
-do so. We want to study complex data which is often multimodal time
-lapse microscopy images of interacting cell populations, without loss of
-generality. With a high need for an easy-to-use,
-no-coding-skill-required software adapted to images and intended for
-biologists, we introduce **Celldetective**, an open-source python-based
-software with the following highlight features:
-
--   **Comprehensive single-cell image analysis** : Celldetective ships
-    segmentation, tracking, and measurement modules, as well as event
-    detection from single-cell signals, for up to two populations of
-    interest.
--   **Integration of state-of-the-art solutions** : Celldetective
-    harnesses state-of-the-art segmentation techniques (StarDist[^1],
-    Cellpose[^2] ,[^3]) and tracking algorithm (bTrack[^4]), as well as
-    the napari viewer[^5] where applicable. These algorithms are
-    interfaced to be well integrated and accessible for the target
-    audience, in the context of complex biological applications.
--   **A framework for event description and annotations** : we propose a
-    broad and intuitive framework to annotate and automate the detection
-    of events from single-cell signals through Deep Learning signal
-    classification and regression. The event formulation is directly
-    exploited to define population survival responses.
--   **A neighborhood scheme to study cell-cell interactions** : we
-    introduce a neighborhood scheme to relate the spatio-temporal
-    distribution and measurements of two cell populations, allowing the
-    study of how cell-cell interactions affect single-cell and
-    population responses.
--   **Deep Learning customization in GUI** : Celldetective facilitates
-    the specialization of Deep Learning models or the creation of new
-    ones adapted to user data, by facilitating the creation of training
-    sets and the training of such models, without having to write a
-    single line of code.
--   **In-software analysis** : Celldetective ships visualization tools
-    to collapse single-cell signals with respect to an event, build
-    survival curves, compare measurement distributions across biological
-    conditions.
--   **A library of segmentation and signal models**: we created specific
-    models to investigate a co-culture of MCF-7 cells and primary NK
-    cells, that are available directly is the software with a large
-    collection of generalist models developed by the StarDist and
-    Cellpose teams, which are a perfect starting point to segment single
-    cells in a new biological system.
--   **Accessible and open source** : Celldetective does not require any
-    coding skills. The software, its models and datasets are made fully
-    open source to encourage transparency and reproducibility.
-
-<embed>
-    <p align="center">
-    <img src="https://github.com/remyeltorro/celldetective/blob/main/docs/source/_static/signal-annotator.gif" width="90%" />
-    </p>
-</embed>
-
-# System requirements
-
-## Hardware requirements
-
-The software was tested on several machines, including:
-
--   An Intel(R) Core(TM) i9-10850K CPU @ 3.60GHz, with a single NVIDIA
-    GeForce RTX 3070 (8 Gb of memory) and 16 Gb of memory
--   An Intel(R) Core(TM) i7-9750H CPU @ 2.60 GHz, with 16 Gb of memory
-
-In GPU mode, succesive segmentation and DL signal analysis could be
-performed without saturating the GPU memory thanks to the subprocess
-formulation for the different modules. The GPU can be disabled in the
-startup window. The software does not require a GPU (but model inference
-will be longer). A typical analysis of a single movie with a GPU takes
-between 5 to 15 minutes. Depending on the number of cells and frames on
-the images, this computation time can increase to the order of half an
-hour on a CPU.
-
-The memory must be sufficient to load a movie stack at once in order to
-visualize it in napari. Otherwise, processing is performed frame by
-frame, therefore the memory required is extremely low.
-
-## Software requirements
-
-The software was developed simulateously on Ubuntu 20.04 and Windows 11.
-It was tested on MacOS, but Tensorflow installation can rquire extra
-steps.
-
--   Linux: Ubuntu 20.04.6 LTS (Focal Fossa) (not tested on ulterior
-    versions)
--   Windows: Windows 11 Home 23H2
-
-To use the software, you must install python, *e.g.* through
-[Anaconda](https://www.anaconda.com/download). We developed and tested
-the software in Python 3.9 and more recently 3.11.
-
-# Installation
-
-## Stable release
-
-Celldetective requires a version of Python between 3.9 and 3.11 (included). If your Python version is older or more recent, consider using `conda` to create an environment as described below.
-
-With the proper Python version, Celldetective can be directly installed with `pip`:
-
-``` bash
-pip install celldetective
-```
-
-We recommend that you create an environment to use Celldetective, to protect your package versions and fix the Python version *e.g.*
-with `conda`:
-
-``` bash
-conda create -n celldetective python=3.11 pyqt
-conda activate celldetective
-pip install celldetective
-```
-
-Need an update? Simply type the following in the terminal (in your
-environment):
-
-``` bash
-pip install --upgrade celldetective
-```
-
-## Development version
-
-### From GitHub
-
-If you want to run the latest development version, you can clone the
-repository to your local machine and install Celldetective in
-"development" mode. This means that any changes to the cloned repository
-will be immediately available in the python environment:
-
-``` bash
-# creates "celldetective" folder
-git clone git://github.com/remyeltorro/celldetective.git
-cd celldetective
-
-# optional: create an environment
-conda create -n celldetective python=3.11 pyqt
-conda activate celldetective
-
-# install the celldetective package in editable/development mode
-pip install -r requirements.txt
-pip install -e .
-```
-
-To run the latest development version without cloning the repository,
-you can also use this line:
-
-``` bash
-pip install git+https//github.com/remyeltorro/celldetective.git
-```
-
-### From a zip file
-
-You can also download the repository as a compressed file. Unzip the
-file and open a terminal at the root of the folder (same level as the
-file requirements.txt). We recommend that you create a python
-environment as Celldetective relies on many packages that may interfere
-with package requirements for other projects. Run the following lines to
-create an environment named \"celldetective\":
-
-``` bash
-conda create -n celldetective python=3.11 pyqt
-conda activate celldetective
-pip install -r requirements.txt
-pip install -e .
-```
-
-The installation of the dependencies will take a few minutes (up to half
-an hour if the network is bad). The Celldetective package itself is
-light and installs in a few seconds.
-
-Before launching the software, move to a different directory as running
-the package locally can create some bugs when locating the models.
-
-# Quick start
-
-You can launch the GUI by 1) opening a terminal and 2) typing the
-following:
-
-``` bash
-python -m celldetective
-```
-
-# Documentation
-
-Read the tutorial here:
-
-<https://celldetective.readthedocs.io/>
-
-# How to cite?
-
-If you use this software in your research, please cite the
-[Celldetective](https://www.biorxiv.org/content/10.1101/2024.03.15.585250v1)
-paper (currently preprint):
-
-``` raw
-@article {Torro2024.03.15.585250,
-    author = {R{\'e}my Torro and Beatriz D{\`\i}az-Bello and Dalia El Arawi and Lorna Ammer and Patrick Chames and Kheya Sengupta and Laurent Limozin},
-    title = {Celldetective: an AI-enhanced image analysis tool for unraveling dynamic cell interactions},
-    elocation-id = {2024.03.15.585250},
-    year = {2024},
-    doi = {10.1101/2024.03.15.585250},
-    publisher = {Cold Spring Harbor Laboratory},
-    abstract = {A current key challenge in bioimaging is the analysis of multimodal and multidimensional data reporting dynamic interactions between diverse cell populations. We developed Celldetective, a software that integrates AI-based segmentation and tracking algorithms and automated signal analysis into a user-friendly graphical interface. It offers complete interactive visualization, annotation, and training capabilities. We demonstrate it by analyzing original experimental data of spreading immune effector cells as well as antibody-dependent cell cytotoxicity events using multimodal fluorescence microscopy.Competing Interest StatementThe authors have declared no competing interest.},
-    URL = {https://www.biorxiv.org/content/early/2024/03/17/2024.03.15.585250},
-    eprint = {https://www.biorxiv.org/content/early/2024/03/17/2024.03.15.585250.full.pdf},
-    journal = {bioRxiv}
-}
-```
-
-Make sure you to cite the papers of any segmentation model (StarDist,
-Cellpose) or tracker (bTrack) you used through Celldetective.
-
-# Bibliography
-
-[^1]: Schmidt, U., Weigert, M., Broaddus, C. & Myers, G. Cell Detection
-    with Star-Convex Polygons. in Medical Image Computing and Computer
-    Assisted Intervention -- MICCAI 2018 (eds. Frangi, A. F., Schnabel,
-    J. A., Davatzikos, C., Alberola-López, C. & Fichtinger, G.) 265--273
-    (Springer International Publishing, Cham, 2018).
-    <doi:10.1007/978-3-030-00934-2_30>.
-
-[^2]: Stringer, C., Wang, T., Michaelos, M. & Pachitariu, M. Cellpose: a
-    generalist algorithm for cellular segmentation. Nat Methods 18,
-    100--106 (2021).
-
-[^3]: Pachitariu, M. & Stringer, C. Cellpose 2.0: how to train your own
-    model. Nat Methods 19, 1634--1641 (2022).
-
-[^4]: Ulicna, K., Vallardi, G., Charras, G. & Lowe, A. R. Automated Deep
-    Lineage Tree Analysis Using a Bayesian Single Cell Tracking
-    Approach. Frontiers in Computer Science 3, (2021).
-
-[^5]: Ahlers, J. et al. napari: a multi-dimensional image viewer for
-    Python. Zenodo <https://doi.org/10.5281/zenodo.8115575> (2023).