diff --git a/.gitignore b/.gitignore
index 322472c..d81b1c7 100755
--- a/.gitignore
+++ b/.gitignore
@@ -85,3 +85,4 @@ examples/_*
examples/_*/
_*/
examples/*demo_data*
+outputs/
diff --git a/CITATION.cff b/CITATION.cff
index 08c390d..761e889 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -1,18 +1,14 @@
cff-version: 1.2.0
-title: >-
- htsimaging: High-Throughput Single-cell Imaging analysis
- in python
-message: >-
- If you use this software, please cite it using the
- metadata from this file.
+title: 'htsimaging: High-Throughput Single-cell Imaging analysis in python'
+message: If you use this software, please cite it using the metadata from this file.
type: software
authors:
- - given-names: Rohan
- family-names: Dandage
- orcid: 'https://orcid.org/0000-0002-6421-2067'
+- given-names: Rohan
+ family-names: Dandage
+ orcid: https://orcid.org/0000-0002-6421-2067
identifiers:
- - type: doi
- value: 10.5281/zenodo.8264035
-repository-code: 'https://github.com/rraadd88/htsimaging'
-version: 1.0.4
-date-released: '2023-08-10'
+- type: doi
+ value: doi/10.5281/zenodo.3697134
+repository-code: https://github.com/rraadd88/htsimaging
+version: v1.0.5
+date-released: '2023-11-27'
diff --git a/README.md b/README.md
index 292c7a3..c34d956 100755
--- a/README.md
+++ b/README.md
@@ -9,7 +9,7 @@
[](https://github.com/rraadd88/htsimaging/issues)
[](https://pepy.tech/project/htsimaging)
-[](https://github.com/rraadd88/htsimaging/blob/master/LICENSE)
+[](https://github.com/rraadd88/htsimaging/blob/main/LICENSE)
@@ -23,8 +23,19 @@
ยท
Explore the API
-
-
+
+
+
+
+# Examples
+
+[๐ Single-cell protein abundance and its normalization](https://github.com/rraadd88/htsimaging/blob/main/examples/protein_abundance_and_normalization.ipynb)
+[๐ Single-cell protein abundance by marker localization](https://github.com/rraadd88/htsimaging/blob/main/examples/protein_abundance_by_marker_location.ipynb)
+[๐ผ๏ธ Visualization of the images.](https://github.com/rraadd88/htsimaging/blob/main/examples/viz_image.ipynb)
+[๐ Quantitative analysis of endocytosis.](https://github.com/rraadd88/htsimaging/blob/main/examples/endocytosis.ipynb)
+[๐ Single-particle tracking (SPT).](https://github.com/rraadd88/htsimaging/blob/main/examples/spt.ipynb)
+[๐ Calculating the recovery rate from a bleach-chase data](https://github.com/rraadd88/htsimaging/blob/main/examples/bleach_chase.ipynb)
+
# Installation
```
@@ -34,14 +45,30 @@ With additional dependencies as required:
```
pip install htsimaging[spt] # for the analysis of the Single-Particle Tracking e.g. endocytosis.
```
-# Examples
+
+# How to cite?
+1. Using BibTeX:
+```
+@software{Dandage_htsimaging,
+ title = {htsimaging: High-Throughput Single-cell Imaging analysis in python},
+ author = {Dandage, Rohan},
+ year = {2023},
+ url = {https://zenodo.org/doi/10.5281/zenodo.3697134},
+ version = {v1.0.5},
+ note = {The URL is a DOI link to the permanent archive of the software.},
+}
+```
+2. DOI link: [](https://zenodo.org/doi/10.5281/zenodo.3697134), or
-[Single-cell protein abundance and its normalization](https://github.com/rraadd88/htsimaging/blob/master/examples/protein_abundance_and_normalization.ipynb)
-[Single-cell protein abundance by marker localization](https://github.com/rraadd88/htsimaging/blob/master/examples/protein_abundance_by_marker_location.ipynb)
-[Visualization of the images.](https://github.com/rraadd88/htsimaging/blob/master/examples/viz_image.ipynb)
-[Quantitative analysis of endocytosis.](https://github.com/rraadd88/htsimaging/blob/master/examples/endocytosis.ipynb)
-[Single-particle tracking (SPT).](https://github.com/rraadd88/htsimaging/blob/master/examples/spt.ipynb)
-[Calculating the recovery rate from a bleach-chase data](https://github.com/rraadd88/htsimaging/blob/master/examples/bleach_chase.ipynb)
+3. Using citation information from [CITATION.CFF file](https://github.com/rraadd88/htsimaging/blob/main/CITATION.cff).
+
+
+# Future directions, for which contributions are welcome
+- [ ] Command-line usage.
+
+# Similar projects
+- https://github.com/vanvalenlab/deepcell-tf
+- https://github.com/junlabucsd/napari-mm3
# API
@@ -1678,208 +1705,6 @@ Distance travelled.
- `pd.DataFrame`: output dataframe.
-
-
-
-
-## module `htsimaging.spt.viz`
-
-
-
-
-
----
-
-
-
-### function `plot_msd`
-
-```python
-plot_msd(
- imsd: DataFrame,
- emsd: DataFrame,
- scale: str = 'log',
- plot_fh: str = None,
- time_points_max: int = None,
- ax: Axes = None
-) โ Axes
-```
-
-Plot MSD.
-
-
-
-**Args:**
-
- - `imsd` (pd.DataFrame): mean squared displacement of each particle.
- - `emsd` (pd.DataFrame): ensemble mean squared displacement of particles.
- - `scale` (str, optional): axis scale. Defaults to "log".
- - `plot_fh` (str, optional): output path. Defaults to None.
- - `params_msd` (dict, optional): parameters of MSD. Defaults to { "mpp":0.0645, "fps":0.2, "max_lagtime":100 }.
- - `ax` (plt.Axes, optional): subplot. Defaults to None.
-
-
-
-**Returns:**
-
- - `plt.Axes`: subplot
-
-
-
-**Examples:**
- Calculate `time_points_max`: ```
- params_msd: dict={
- "mpp":0.0645,
- "fps":0.2,
- "max_lagtime":100
- }
- time_points_max=params_msd["fps"]*params_msd["max_lagtime"]
- ```
-
-
----
-
-
-
-### function `plot_emsd`
-
-```python
-plot_emsd(
- expt_data: DataFrame,
- color: str = 'k',
- scale: str = 'log',
- plot_fh: str = None,
- ax: Axes = None
-) โ Axes
-```
-
-Plot ensemble mean squared displacement of particles.
-
-
-
-**Args:**
-
- - `expt_data` (pd.DataFrame): input data.
- - `color` (str, optional): color. Defaults to 'k'.
- - `scale` (str, optional): scale of the axes. Defaults to "log".
- - `plot_fh` (str, optional): output path. Defaults to None.
- - `ax` (plt.Axes, optional): subplot. Defaults to None.
-
-
-
-**Returns:**
-
- - `plt.Axes`: subplot
-
-
----
-
-
-
-### function `plot_kin`
-
-```python
-plot_kin(
- traj: DataFrame,
- dparams: DataFrame = None,
- ctime: str = 'time (s)',
- fit_eqn: str = None,
- ylabel: str = '',
- label: str = '',
- color: str = 'b',
- ax1: Axes = None,
- plot_fh: str = None
-) โ Axes
-```
-
-Plot kinetics.
-
-
-
-**Args:**
-
- - `traj` (pd.DataFrame): table containing the trajectories.
- - `dparams` (pd.DataFrame, optional): table containing the parameters. Defaults to None.
- - `ctime` (str, optional): time point. Defaults to 'time (s)'.
- - `fit_eqn` (str, optional): fit equation name. Defaults to None.
-
-
-
-**Returns:**
- plt.Axes
-
-
----
-
-
-
-### function `plot_kin_all`
-
-```python
-plot_kin_all(expt_dh: str, imsd_fhs: list)
-```
-
-Plot multiple kinetics plots.
-
-
----
-
-
-
-### function `plot_trajectories_stats`
-
-```python
-plot_trajectories_stats(
- df: DataFrame,
- coly: str,
- colx: str = 'frame',
- rescalex: bool = True,
- label: str = None,
- axvlinex=None,
- params_plot: dict = {'color': 'k', 'alpha': 0.5},
- fig=None,
- ax: Axes = None
-) โ Axes
-```
-
-Plot statistics of the particle trajectories.
-
-
----
-
-
-
-### function `plot_trajectories`
-
-```python
-plot_trajectories(
- traj,
- image,
- colorby: str = 'particle',
- mpp: float = None,
- label: str = False,
- cmap: str = None,
- t_column: str = None,
- pos_columns: list = None,
- plot_style: dict = {},
- params_text: dict = {'ha': 'center', 'va': 'center'},
- ax: Axes = None,
- **kwargs
-) โ Axes
-```
-
-Plot traces of trajectories for each particle. Optionally image it on a frame from the video.
-
-Parameters
----------- traj : DataFrame The DataFrame should include time and spatial coordinate columns. colorby : {'particle', 'frame'}, optional mpp : float, optional Microns per pixel. If omitted, the labels will have units of pixels. label : boolean, optional Set to True to write particle ID numbers next to trajectories. image : ndarray, optional Background image, default None cmap : colormap, optional This is only used in colorby='frame' mode. Default = mpl.cm.winter ax : matplotlib axes object, optional Defaults to current axes t_column : string, optional DataFrame column name for time coordinate. Default is 'frame'. pos_columns : list of strings, optional Dataframe column names for spatial coordinates. Default is ['x', 'y']. plot_style : dictionary Keyword arguments passed through to the `Axes.plot(...)` command
-
-Returns
-------- Axes object
-
-See Also
--------- plot_traj3d : the 3D equivalent of `plot_traj`
-
-
@@ -1954,7 +1779,7 @@ Keyword Args: parameters provided to the `plt.imshow`.
---
-
+
### function `annot_cells`
@@ -1980,7 +1805,7 @@ Annotate the cells on an image.
---
-
+
### function `image_regions_annotated`
diff --git a/examples/endocytosis.ipynb b/examples/endocytosis.ipynb
index 6135db2..7a72531 100755
--- a/examples/endocytosis.ipynb
+++ b/examples/endocytosis.ipynb
@@ -6,7 +6,7 @@
"metadata": {},
"source": [
"---\n",
- "# Quantitative analysis of endocytosis.\n",
+ "# ๐ Quantitative analysis of endocytosis.\n",
"\n",
"Note: Demo data used in this notebook is not included in the repository, but can be made available upon request."
]
diff --git a/examples/image.png b/examples/image.png
new file mode 100644
index 0000000..4690e0e
Binary files /dev/null and b/examples/image.png differ
diff --git a/examples/io_read_nd2.ipynb b/examples/io_read_nd2.ipynb
index 5c8aa1c..baec6ba 100755
--- a/examples/io_read_nd2.ipynb
+++ b/examples/io_read_nd2.ipynb
@@ -6,7 +6,7 @@
"metadata": {},
"source": [
"---\n",
- "## Reading the channels from Nikon microscope images with `.nd2` format"
+ "## ๐พ Reading the channels from Nikon microscope images with `.nd2` format"
]
},
{
diff --git a/examples/protein_abundance_and_normalization.ipynb b/examples/protein_abundance_and_normalization.ipynb
index e9205c3..137e525 100755
--- a/examples/protein_abundance_and_normalization.ipynb
+++ b/examples/protein_abundance_and_normalization.ipynb
@@ -6,7 +6,7 @@
"metadata": {},
"source": [
"---\n",
- "# Single-cell protein abundance and its normalization"
+ "# ๐ Single-cell protein abundance and its normalization"
]
},
{
diff --git a/examples/protein_abundance_by_marker_location.ipynb b/examples/protein_abundance_by_marker_location.ipynb
index 2232f54..7ece8e3 100755
--- a/examples/protein_abundance_by_marker_location.ipynb
+++ b/examples/protein_abundance_by_marker_location.ipynb
@@ -6,7 +6,7 @@
"metadata": {},
"source": [
"---\n",
- "# Single-cell protein abundance by marker localization"
+ "# ๐ Single-cell protein abundance by marker localization"
]
},
{
diff --git a/examples/spt.ipynb b/examples/spt.ipynb
index 40114f7..79e2949 100755
--- a/examples/spt.ipynb
+++ b/examples/spt.ipynb
@@ -5,7 +5,7 @@
"metadata": {},
"source": [
"---\n",
- "## Single-particle tracking (SPT).\n",
+ "## ๐ Single-particle tracking (SPT).\n",
"\n",
"**Demo data** \n",
"Download the demodata from this link: [the test video from Munder et al 2016 paper](https://elifesciences.org/download/aHR0cHM6Ly9zdGF0aWMtbW92aWUtdXNhLmdsZW5jb2Vzb2Z0d2FyZS5jb20vbXA0LzEwLjc1NTQvNTI2LzY3YWIyOTExMjkxMTcyMGU1OTk4MjY5OGZiMWVlMzY2OTE0YTBmZDIvZWxpZmUtMDkzNDctbWVkaWExLm1wNA==/elife-09347-media1.mp4?_hash=0Xnr7HGX1AYuIfQcupU%2BW3PG30wh8Wj6Cx3CXW6cO%2BA%3D) and store it in folder containing this notebook i.e. `examples`.\n",
diff --git a/examples/viz_image.ipynb b/examples/viz_image.ipynb
index f23fc26..33362a1 100755
--- a/examples/viz_image.ipynb
+++ b/examples/viz_image.ipynb
@@ -6,7 +6,7 @@
"metadata": {},
"source": [
"---\n",
- "## Visualization of the images."
+ "## ๐ผ๏ธ Visualization of the images."
]
},
{
@@ -96,7 +96,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.10.8"
+ "version": "3.7.12"
}
},
"nbformat": 4,
diff --git a/setup.py b/setup.py
index 277beb9..e04ae90 100755
--- a/setup.py
+++ b/setup.py
@@ -67,7 +67,7 @@
author='rraadd88',
author_email='rohanadandage@gmail.com',
license='General Public License v. 3',
- packages=setuptools.find_packages('.',exclude=['test', 'unit','deps', 'data']),
+ packages=setuptools.find_packages('.',exclude=['test','tests', 'unit','deps','data','examples']),
classifiers=[
'Programming Language :: Python',
'Programming Language :: Python :: 3',