Merge pull request #62 from fish-quant/develop

v0.6.1

.codecov.yml

@@ -2,11 +2,9 @@ comment: false
 
 ignore:
   - "setup.py"
-  - "python_scripts"
   - "bigfish/plot"
   - "bigfish/deep_learning"
-  - "data"
-  - "weights"
+  - "bigfish/weights"
 
 coverage:
   status:

.travis.yml

@@ -2,8 +2,12 @@ language: python
 
 python:
     - "3.6"
+    - "3.7"
+    - "3.8"
+    - "3.9"
 
 install:
+    - pip install -r requirements.txt
     - pip install -r requirements_dev.txt
 
 script:

README.md

@@ -1,10 +1,11 @@
 # Big-FISH
 
+[![PyPI version](https://badge.fury.io/py/big-fish.svg)](https://badge.fury.io/py/big-fish)
 [![Build Status](https://travis-ci.com/fish-quant/big-fish.svg?branch=master)](https://travis-ci.com/fish-quant/big-fish)
-[![Documentation Status](https://readthedocs.org/projects/big-fish/badge/?version=latest)](https://big-fish.readthedocs.io/en/latest/?badge=latest)
+[![Documentation Status](https://readthedocs.org/projects/big-fish/badge/?version=stable)](https://big-fish.readthedocs.io/en/latest/?badge=stable)
 [![codecov](https://codecov.io/gh/fish-quant/big-fish/branch/master/graph/badge.svg)](https://codecov.io/gh/fish-quant/big-fish)
 [![License](https://img.shields.io/badge/license-BSD%203--Clause-green)](https://github.com/fish-quant/big-fish/blob/master/LICENSE)
-[![Python 3.6](https://img.shields.io/badge/python-3.6-blue.svg)](https://www.python.org/downloads/release/python-360/)
+[![Python version](https://img.shields.io/pypi/pyversions/big-fish.svg)](https://pypi.python.org/pypi/big-fish/)
 
 **Big-FISH** is a python package for the analysis of smFISH images. It includes various methods to **analyze microscopy images**, such **spot detection** and **segmentation of cells and nuclei**. The package allows the user represent the extract properties of a cell as coordinates (see figure below). The ultimate goal is to simplify **large scale statistical analysis** and quantification.
 
@@ -18,20 +19,18 @@
 
 Big-FISH requires Python 3.6 or newer. Additionally, it has the following dependencies:
 
-- numpy (== 1.16.0)
-- scipy (== 1.4.1)
-- scikit-learn (== 0.21.0)
-- scikit-image (== 0.14.2)
-- matplotlib (== 3.0.2)
-- pandas (== 0.24.0)
-- mrc (== 0.1.5)
+- numpy (>= 1.16.0)
+- scipy (>= 1.4.1)
+- scikit-learn (>= 0.21.0)
+- scikit-image (>= 0.14.2)
+- matplotlib (>= 3.0.2)
+- pandas (>= 0.24.0)
+- mrc (>= 0.1.5)
 
 For segmentation purpose, two additional dependencies can be requested:
 - tensorflow (== 2.3.0)
 - tensorflow-addons (== 0.12.1)
 
-Updated dependencies are not tested yet and might break.
-
 ### Virtual environment
 
 To avoid dependency conflicts, we recommend the the use of a dedicated [virtual](https://docs.python.org/3.6/library/venv.html) or [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html) environment.  In a terminal run the command:
@@ -75,6 +74,8 @@ If you have any question relative to the repository, please open an [issue](http
 
 Version 1.0.0:
 - Complete code coverage.
+- Unpin deep learning dependencies
+- Add a pretrained pattern recognition model
 
 ## Development
 
@@ -100,8 +101,14 @@ Please make sure to update tests as appropriate if you open a pull request. You
 pip install -r requirements_dev.txt
 ```
 
-To perform unitary tests, run : 
+To perform unit tests, run : 
 
 ```bash
 pytest bigfish
 ```
+
+## Citation
+
+If you exploit this package for your work, please cite:
+
+> Arthur Imbert, Wei Ouyang, Adham Safieddine, Emeline Coleno, Christophe Zimmer, Edouard Bertrand, Thomas Walter, Florian Mueller. FISH-quant v2: a scalable and modular analysis tool for smFISH image analysis. bioRxiv (2021) https://doi.org/10.1101/2021.07.20.453024

bigfish/__init__.py

@@ -12,4 +12,4 @@
 # MINOR: new features
 # PATCH: backwards compatible bug fixes
 # MAJOR.MINOR.PATCHdev means a version under development
-__version__ = "0.6.0"
+__version__ = "0.6.1"

bigfish/detection/spot_detection.py

@@ -563,7 +563,7 @@ def _get_spot_counts(thresholds, value_spots):
     thresholds : np.ndarray, np.float64
         Candidate threshold values.
     count_spots : np.ndarray, np.float64
-        Spots count function.
+        Spots count function (log scale).
 
     """
     # count spots for each threshold
@@ -616,7 +616,7 @@ def get_elbow_values(images, voxel_size=None, spot_radius=None,
     thresholds : np.ndarray, np.float64
         Candidate threshold values.
     count_spots : np.ndarray, np.float64
-        Spots count.
+        Spots count (log scale).
     threshold : float or None
         Threshold automatically set.
 

bigfish/multistack/postprocess.py

@@ -518,6 +518,7 @@ def _check_nucleus_in_cell(cell_mask, nuc_mask):
         return True
 
 
+# TODO fix docstring
 def extract_spots_from_frame(spots, z_lim=None, y_lim=None, x_lim=None):
     """Get spots coordinates within a given frame.
 
@@ -567,7 +568,8 @@ def extract_spots_from_frame(spots, z_lim=None, y_lim=None, x_lim=None):
     return extracted_spots
 
 
-def summarize_extraction_results(fov_results, ndim, path_output=None):
+def summarize_extraction_results(fov_results, ndim, path_output=None,
+                                 delimiter=";"):
     """Summarize results extracted from an image and store them in a dataframe.
 
     Parameters
@@ -584,8 +586,11 @@ def summarize_extraction_results(fov_results, ndim, path_output=None):
         * `cell_mask`: mask of the cell.
     ndim : int
         Number of spatial dimensions to consider (2 or 3).
-    path_output : str or None
+    path_output : str, optional
         Path to save the dataframe in a csv file.
+    delimiter : str, default=";"
+        Delimiter used to separate columns if the dataframe is saved in a csv
+        file.
 
     Returns
     -------
@@ -613,7 +618,7 @@ def summarize_extraction_results(fov_results, ndim, path_output=None):
     if len(fov_results) == 0:
         df = pd.DataFrame({"cell_id": []})
         if path_output is not None:
-            stack.save_data_to_csv(df, path_output)
+            stack.save_data_to_csv(df, path_output, delimiter)
         return df
 
     # check extra coordinates to summarize
@@ -690,7 +695,7 @@ def summarize_extraction_results(fov_results, ndim, path_output=None):
 
     # save dataframe
     if path_output is not None:
-        stack.save_data_to_csv(df, path_output)
+        stack.save_data_to_csv(df, path_output, delimiter)
 
     return df
 

bigfish/multistack/preprocess.py

@@ -634,4 +634,3 @@ def _load_stack_no_recipe(paths, input_dimension=None):
                          "5 dimensions.".format(input_dimension))
 
     return tensor_5d
-

bigfish/multistack/utils.py

@@ -344,4 +344,3 @@ def check_datamap(data_map):
         check_recipe(recipe, data_directory=input_folder)
 
     return True
-