celldetective 1.0.2__tar.gz → 1.1.0__tar.gz

celldetective-1.1.0/PKG-INFO

@@ -0,0 +1,306 @@
+Metadata-Version: 2.1
+Name: celldetective
+Version: 1.1.0
+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==5.0.2
+Requires-Dist: jinja2<3.1
+Requires-Dist: ipykernel
+Requires-Dist: stardist
+Requires-Dist: cellpose<3
+Requires-Dist: scikit-learn
+Requires-Dist: btrack
+Requires-Dist: tensorflow<=2.12.1
+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~=1.2.2
+Requires-Dist: superqt[cmap]>=0.6.1
+Requires-Dist: setuptools
+Requires-Dist: matplotlib_scalebar
+
+# 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 3.9.18.
+
+# Installation
+
+## Stable release
+
+Celldetective can be installed with `pip`:
+
+``` bash
+pip install celldetective
+```
+
+We recommend that you create an environment to use Celldetective, *e.g.*
+with `conda`:
+
+``` bash
+conda create -n celldetective python=3.9.18 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
+
+# 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=3.9.18 pyqt
+conda activate celldetective
+pip install -r requirements.txt
+pip install .
+```
+
+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).

celldetective-1.1.0/README.md

@@ -0,0 +1,267 @@
+# 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 3.9.18.
+
+# Installation
+
+## Stable release
+
+Celldetective can be installed with `pip`:
+
+``` bash
+pip install celldetective
+```
+
+We recommend that you create an environment to use Celldetective, *e.g.*
+with `conda`:
+
+``` bash
+conda create -n celldetective python=3.9.18 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
+
+# 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=3.9.18 pyqt
+conda activate celldetective
+pip install -r requirements.txt
+pip install .
+```
+
+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).

{celldetective-1.0.2 → celldetective-1.1.0}/celldetective/__main__.py

@@ -15,10 +15,10 @@ class AppInitWindow(QMainWindow):
 	Initial window to set the experiment folder or create a new one.
 	"""
 
-	def __init__(self, parent=None):
+	def __init__(self, parent_window=None):
 		super().__init__()
 
-		self.parent = parent
+		self.parent_window = parent_window
 		self.Styles = Styles()
 		self.init_styles()
 		self.setWindowTitle("celldetective")

{celldetective-1.0.2 → celldetective-1.1.0}/celldetective/events.py

@@ -1,49 +1,7 @@
 import numpy as np
 
-def switch_to_events(classes, times, max_times, first_detections=None, left_censored=False, FrameToMin=None):
-	
-	events = []
-	survival_times = []
-	if first_detections is None:
-		first_detections = np.zeros_like(max_times)
-		
-	for c,t,mt,ft in zip(classes, times, max_times, first_detections):
-
-		if left_censored:
-			#print('left censored is True: exclude cells that exist in first frame')
-			if ft>0.:
-				if c==0:
-					if t>0:
-						dt = t - ft
-						#print('event: dt = ',dt, t, ft)
-						if dt>0:
-							events.append(1)
-							survival_times.append(dt)
-				elif c==1:
-					dt = mt - ft
-					if dt>0:
-						events.append(0)
-						survival_times.append(dt)
-				else:
-					pass
-		else:
-			if c==0:
-				if t>0:
-					events.append(1)
-					survival_times.append(t - ft)
-			elif c==1:
-				events.append(0)
-				survival_times.append(mt - ft)
-			else:
-				pass
 
-	if FrameToMin is not None:
-		print('convert to minutes!', FrameToMin)
-		survival_times = [s*FrameToMin for s in survival_times]
-	return events, survival_times
-	  
-	
-def switch_to_events_v2(classes, event_times, max_times, origin_times=None, left_censored=True, FrameToMin=None):
+def switch_to_events(classes, event_times, max_times, origin_times=None, left_censored=True, FrameToMin=None):
 	
 
 	"""
@@ -144,6 +102,6 @@ def switch_to_events_v2(classes, event_times, max_times, origin_times=None, left
 				pass
 
 	if FrameToMin is not None:
-		print('convert to minutes!', FrameToMin)
+		#print('convert to minutes!', FrameToMin)
 		survival_times = [s*FrameToMin for s in survival_times]
 	return events, survival_times

{celldetective-1.0.2 → celldetective-1.1.0}/celldetective/filters.py

@@ -35,8 +35,8 @@ def variance_filter(img, size):
 
 	size = int(size)
 	img = img.astype(float)
-	win_mean = snd.uniform_filter(img, (size,size))
-	win_sqr_mean = snd.uniform_filter(img**2, (size,size))
+	win_mean = snd.uniform_filter(img, (size,size), mode='wrap')
+	win_sqr_mean = snd.uniform_filter(img**2, (size,size), mode='wrap')
 	img = win_sqr_mean - win_mean**2
 
 	return img
@@ -45,8 +45,8 @@ def std_filter(img, size):
 
 	size = int(size)
 	img = img.astype(float)
-	win_mean = snd.uniform_filter(img, (size,size))
-	win_sqr_mean = snd.uniform_filter(img**2, (size, size))
+	win_mean = snd.uniform_filter(img, (size,size), mode='wrap')
+	win_sqr_mean = snd.uniform_filter(img**2, (size, size), mode='wrap')
 	win_sqr_mean[win_sqr_mean!=win_sqr_mean] = 0.
 	win_sqr_mean[win_sqr_mean<=0.] = 0. # add this to prevent sqrt from breaking
 	img = np.sqrt(win_sqr_mean - win_mean**2)
@@ -65,7 +65,6 @@ def otsu_filter(img, *kwargs):
 	return binary.astype(float)
 
 def local_filter(img, *kwargs):
-	print(*kwargs)
 	thresh = threshold_local(img.astype(float), *kwargs)
 	binary = img >= thresh
 	return binary.astype(float)

{celldetective-1.0.2 → celldetective-1.1.0}/celldetective/gui/__init__.py

@@ -13,7 +13,7 @@ from .retrain_signal_model_options import ConfigSignalModelTraining
 from .retrain_segmentation_model_options import ConfigSegmentationModelTraining
 from .thresholds_gui import ThresholdConfigWizard
 from .seg_model_loader import SegmentationModelLoader
-from .process_block import ProcessPanel, NeighPanel
+from .process_block import ProcessPanel, NeighPanel, PreprocessingPanel
 from .analyze_block import AnalysisPanel
 from .control_panel import ControlPanel
 from .configure_new_exp import ConfigNewExperiment