vlab4mic 0.0.12__tar.gz

vlab4mic-0.0.12/LICENSE.txt

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 [Ricardo Henriques <ricardo@henriqueslab.org>]
+
+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.

vlab4mic-0.0.12/PKG-INFO

@@ -0,0 +1,211 @@
+Metadata-Version: 2.4
+Name: vlab4mic
+Version: 0.0.12
+Summary: VLab4Mic: A virtual laboratory for microscopy simulation and validation
+Author-email: Damián Martinez <jdmartinezigc@gmail.com>, Bruno Saraiva <bruno.msaraiva2@gmail.com>, Mario del Rosario <mario.delrosario@itqb.unl.pt>, Ricardo Henriques <ricardo@henriqueslab.org>
+License: MIT
+Classifier: Programming Language :: Python :: 3.11
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE.txt
+Requires-Dist: numpy>=1.26.4
+Requires-Dist: matplotlib>=3.9.0
+Requires-Dist: scipy>=1.13.1
+Requires-Dist: biopython>=1.83
+Requires-Dist: plotly>=5.22.0
+Requires-Dist: trimesh>=4.4.0
+Requires-Dist: pyyaml>=6.0.1
+Requires-Dist: tifffile>=2024.5.22
+Requires-Dist: tqdm>=4.66.4
+Requires-Dist: scikit-image>=0.23.2
+Requires-Dist: requests>=2.32.3
+Requires-Dist: scikit-learn>=1.5.0
+Requires-Dist: pandas>=2.2.3
+Requires-Dist: seaborn>=0.13.2
+Requires-Dist: opencv-python>=4.11
+Provides-Extra: all
+Requires-Dist: vlab4mic[dev,test]; extra == "all"
+Provides-Extra: dev
+Requires-Dist: pre-commit>=3.7.0; extra == "dev"
+Requires-Dist: ruff>=0.4.3; extra == "dev"
+Requires-Dist: gptrepo>=1.0.3; extra == "dev"
+Requires-Dist: pdoc>=12.3.1; extra == "dev"
+Requires-Dist: build; extra == "dev"
+Provides-Extra: test
+Requires-Dist: pytest>=8.2.0; extra == "test"
+Requires-Dist: pytest-xdist>=3.6.1; extra == "test"
+Requires-Dist: pytest-cov>=5.0.0; extra == "test"
+Requires-Dist: nbmake>=1.5.3; extra == "test"
+Requires-Dist: mypy>=1.10.0; extra == "test"
+Dynamic: license-file
+
+# VLab4Mic: A Virtual Laboratory for Microscopy  
+*A friendly toolkit to help researchers simulate fluorescence microscopy images, no coding required.*
+
+<img src="src/logo/logo.png" align="right" width="180" style="margin-left: 20px;"/>
+
+VLab4Mic lets you explore, test, and validate imaging experiments **before stepping into the microscope room**.  
+Whether you are new to Python or an experienced bioimage researcher, VLab4Mic provides a safe sandbox to:
+
+- Build **virtual samples** from PDB/CIF structures  
+- Apply **direct or indirect fluorescent labeling**  
+- Introduce **defects**, crowding, and structural variation  
+- Simulate image acquisition across modalities  
+- Run **parameter sweeps** to explore experimental conditions  
+- Compare **noiseless vs. realistic** acquisitions  
+
+This README is written to be friendly for beginners while maintaining the technical depth experienced users expect.
+
+<img src="examples/Tutorial1.gif"/>
+
+
+# Who Is This Tool For?
+
+- **New microscopy users:** to gain intuitive understanding without coding  
+- **Researchers designing experiments:** testing probes, PSFs, exposure times  
+- **Microscopy experts:** benchmarking reconstruction methods or PSFs  
+
+---
+
+# 🚀 Quick Start Options
+
+| Option | Skills Needed | Best For |
+|-------|----------------|----------|
+| **1. Google Colab** | None | Beginners, teaching, quick experiments |
+| **2. Local Jupyter Notebooks** | Basic installation | Smooth widget-based use |
+| **3. Python Scripts** | Comfortable with code | Full flexibility & automation |
+
+---
+
+# 🟢 Option 1 — Google Colab (No Installation Needed)
+
+The easiest way to start.
+
+✔ No installation  
+✔ No configuration  
+✔ Works in browser  
+✔ Always up to date  
+
+### 👉 Click to open the main notebook:
+| Category | Description | Notebook | Colab |
+|---------|-------------|----------|-------|
+| **Main Interface** | Create virtual samples & simulate imaging | [Notebook](https://github.com/HenriquesLab/VLab4Mic/blob/main/notebooks/VLab4Mic_main.ipynb) | [Open in Colab](https://githubtocolab.com/HenriquesLab/VLab4Mic/blob/main/notebooks/VLab4Mic_main.ipynb) |
+| **Parameter Sweeps** | Configure & run simulation sweeps | [Notebook](https://github.com/HenriquesLab/VLab4Mic/blob/main/notebooks/VLab4Mic_parameter_sweeps.ipynb) | [Open in Colab](https://githubtocolab.com/HenriquesLab/VLab4Mic/blob/main/notebooks/VLab4Mic_parameter_sweeps.ipynb) |
+
+### If the Colab link fails:
+1. Click the **Jupyter** badge (opens the raw notebook)  
+2. Download the `.ipynb` file  
+3. Open Google Colab → **File → Upload notebook**  
+
+---
+
+# 🔵 Option 2 — Local Installation (Beginner-Friendly)
+
+### 1️⃣ Create a virtual environment  
+You may use Conda or similar.
+
+#### Using Conda:
+Run the following command (replace `MYENV` with your desired environment name):
+
+```bash
+conda create --name MYENV python=3.11
+```
+
+Then activate it:
+```bash
+conda activate MYENV
+```
+
+---
+
+### 2️⃣ Install VLab4Mic and its associated library to use the codeless jupyter notebooks
+```bash
+pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple vlab4mic vlab4micjupyter
+```
+
+---
+
+### 3️⃣ Launch Jupyter Lab
+```bash
+jupyter lab
+```
+
+---
+
+### 4️⃣ Download and open notebooks  
+From:  
+https://github.com/HenriquesLab/VLab4Mic/tree/main/notebooks
+
+---
+
+# 🔴 Option 3 — Use VLab4Mic as a Python Library (Advanced)
+
+Example script:
+
+```python
+from vlab4mic.experiments import image_vsample
+import matplotlib.pyplot as plt
+
+modalities = ["Widefield", "Confocal", "STED"]
+
+images, noiseless, experiment = image_vsample(
+    structure="7R5K",
+    probe_template="Antibody",
+    probe_target_type="Sequence",
+    probe_target_value="ELAVGSL",
+    multimodal=modalities,
+    number_of_particles=10,
+    run_simulation=True,
+)
+
+fig, axs = plt.subplots(1, len(modalities))
+for i, mod in enumerate(modalities):
+    axs[i].imshow(images[mod][0], cmap="magma")
+    axs[i].set_title(mod)
+plt.show()
+```
+
+For more examples see `/examples`.
+
+---
+
+# Documentation & Manual
+
+- Full Manual: https://github.com/HenriquesLab/VLab4Mic/blob/main/manual.md  
+- Wiki Tutorials: https://github.com/HenriquesLab/VLab4Mic/wiki  
+
+---
+
+# Core Features
+
+### ✔ Structural modelling  
+### ✔ Virtual sample creation  
+### ✔ Imaging simulations  
+### ✔ Parameter sweeps  
+### ✔ Widget-based GUI  
+### ✔ Flexible Python API  
+
+---
+
+# Troubleshooting
+
+**Jupyter won't open →** Environment not activated.  
+**ImportError →** Install VLab4Mic inside the active environment.  
+**Colab won't load →** Upload notebook manually.  
+
+If issues persist, open an issue!
+
+---
+
+# Contributing
+Contributions welcome!  
+See: https://github.com/HenriquesLab/VLab4Mic/blob/main/CONTRIBUTING.md
+
+# Support
+- Discussions: https://github.com/HenriquesLab/VLab4Mic/discussions  
+- Issues: https://github.com/HenriquesLab/VLab4Mic/issues  
+
+
+

vlab4mic-0.0.12/README.md

@@ -0,0 +1,168 @@
+# VLab4Mic: A Virtual Laboratory for Microscopy  
+*A friendly toolkit to help researchers simulate fluorescence microscopy images, no coding required.*
+
+<img src="src/logo/logo.png" align="right" width="180" style="margin-left: 20px;"/>
+
+VLab4Mic lets you explore, test, and validate imaging experiments **before stepping into the microscope room**.  
+Whether you are new to Python or an experienced bioimage researcher, VLab4Mic provides a safe sandbox to:
+
+- Build **virtual samples** from PDB/CIF structures  
+- Apply **direct or indirect fluorescent labeling**  
+- Introduce **defects**, crowding, and structural variation  
+- Simulate image acquisition across modalities  
+- Run **parameter sweeps** to explore experimental conditions  
+- Compare **noiseless vs. realistic** acquisitions  
+
+This README is written to be friendly for beginners while maintaining the technical depth experienced users expect.
+
+<img src="examples/Tutorial1.gif"/>
+
+
+# Who Is This Tool For?
+
+- **New microscopy users:** to gain intuitive understanding without coding  
+- **Researchers designing experiments:** testing probes, PSFs, exposure times  
+- **Microscopy experts:** benchmarking reconstruction methods or PSFs  
+
+---
+
+# 🚀 Quick Start Options
+
+| Option | Skills Needed | Best For |
+|-------|----------------|----------|
+| **1. Google Colab** | None | Beginners, teaching, quick experiments |
+| **2. Local Jupyter Notebooks** | Basic installation | Smooth widget-based use |
+| **3. Python Scripts** | Comfortable with code | Full flexibility & automation |
+
+---
+
+# 🟢 Option 1 — Google Colab (No Installation Needed)
+
+The easiest way to start.
+
+✔ No installation  
+✔ No configuration  
+✔ Works in browser  
+✔ Always up to date  
+
+### 👉 Click to open the main notebook:
+| Category | Description | Notebook | Colab |
+|---------|-------------|----------|-------|
+| **Main Interface** | Create virtual samples & simulate imaging | [Notebook](https://github.com/HenriquesLab/VLab4Mic/blob/main/notebooks/VLab4Mic_main.ipynb) | [Open in Colab](https://githubtocolab.com/HenriquesLab/VLab4Mic/blob/main/notebooks/VLab4Mic_main.ipynb) |
+| **Parameter Sweeps** | Configure & run simulation sweeps | [Notebook](https://github.com/HenriquesLab/VLab4Mic/blob/main/notebooks/VLab4Mic_parameter_sweeps.ipynb) | [Open in Colab](https://githubtocolab.com/HenriquesLab/VLab4Mic/blob/main/notebooks/VLab4Mic_parameter_sweeps.ipynb) |
+
+### If the Colab link fails:
+1. Click the **Jupyter** badge (opens the raw notebook)  
+2. Download the `.ipynb` file  
+3. Open Google Colab → **File → Upload notebook**  
+
+---
+
+# 🔵 Option 2 — Local Installation (Beginner-Friendly)
+
+### 1️⃣ Create a virtual environment  
+You may use Conda or similar.
+
+#### Using Conda:
+Run the following command (replace `MYENV` with your desired environment name):
+
+```bash
+conda create --name MYENV python=3.11
+```
+
+Then activate it:
+```bash
+conda activate MYENV
+```
+
+---
+
+### 2️⃣ Install VLab4Mic and its associated library to use the codeless jupyter notebooks
+```bash
+pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple vlab4mic vlab4micjupyter
+```
+
+---
+
+### 3️⃣ Launch Jupyter Lab
+```bash
+jupyter lab
+```
+
+---
+
+### 4️⃣ Download and open notebooks  
+From:  
+https://github.com/HenriquesLab/VLab4Mic/tree/main/notebooks
+
+---
+
+# 🔴 Option 3 — Use VLab4Mic as a Python Library (Advanced)
+
+Example script:
+
+```python
+from vlab4mic.experiments import image_vsample
+import matplotlib.pyplot as plt
+
+modalities = ["Widefield", "Confocal", "STED"]
+
+images, noiseless, experiment = image_vsample(
+    structure="7R5K",
+    probe_template="Antibody",
+    probe_target_type="Sequence",
+    probe_target_value="ELAVGSL",
+    multimodal=modalities,
+    number_of_particles=10,
+    run_simulation=True,
+)
+
+fig, axs = plt.subplots(1, len(modalities))
+for i, mod in enumerate(modalities):
+    axs[i].imshow(images[mod][0], cmap="magma")
+    axs[i].set_title(mod)
+plt.show()
+```
+
+For more examples see `/examples`.
+
+---
+
+# Documentation & Manual
+
+- Full Manual: https://github.com/HenriquesLab/VLab4Mic/blob/main/manual.md  
+- Wiki Tutorials: https://github.com/HenriquesLab/VLab4Mic/wiki  
+
+---
+
+# Core Features
+
+### ✔ Structural modelling  
+### ✔ Virtual sample creation  
+### ✔ Imaging simulations  
+### ✔ Parameter sweeps  
+### ✔ Widget-based GUI  
+### ✔ Flexible Python API  
+
+---
+
+# Troubleshooting
+
+**Jupyter won't open →** Environment not activated.  
+**ImportError →** Install VLab4Mic inside the active environment.  
+**Colab won't load →** Upload notebook manually.  
+
+If issues persist, open an issue!
+
+---
+
+# Contributing
+Contributions welcome!  
+See: https://github.com/HenriquesLab/VLab4Mic/blob/main/CONTRIBUTING.md
+
+# Support
+- Discussions: https://github.com/HenriquesLab/VLab4Mic/discussions  
+- Issues: https://github.com/HenriquesLab/VLab4Mic/issues  
+
+
+

vlab4mic-0.0.12/pyproject.toml

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+[build-system]
+requires = ["setuptools>=42", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "vlab4mic"
+version = "0.0.12"
+description = "VLab4Mic: A virtual laboratory for microscopy simulation and validation"
+authors = [
+    { name = "Damián Martinez", email = "jdmartinezigc@gmail.com" },
+    { name = "Bruno Saraiva", email = "bruno.msaraiva2@gmail.com" },
+    { name = "Mario del Rosario", email = "mario.delrosario@itqb.unl.pt" },
+    { name = "Ricardo Henriques", email = "ricardo@henriqueslab.org" }
+]
+readme = { file = "README.md", content-type = "text/markdown" }
+license = { text = "MIT" }
+requires-python = ">=3.9"
+classifiers = [
+    "Programming Language :: Python :: 3.11",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent"
+]
+dependencies = [
+    "numpy>=1.26.4",
+    "matplotlib>=3.9.0",
+    "scipy>=1.13.1",
+    "biopython>=1.83",
+    "plotly>=5.22.0",
+    "trimesh>=4.4.0",
+    "pyyaml>=6.0.1",
+    "tifffile>=2024.5.22",
+    "tqdm>=4.66.4",
+    "scikit-image>=0.23.2",
+    "requests>=2.32.3",
+    "scikit-learn>=1.5.0",
+    "pandas>=2.2.3",
+    "seaborn>=0.13.2",
+    "opencv-python>=4.11"
+]
+
+[project.optional-dependencies]
+all = ["vlab4mic[dev,test]"]
+dev = [
+    "pre-commit>=3.7.0",
+    "ruff>=0.4.3",
+    "gptrepo>=1.0.3",
+    "pdoc>=12.3.1",
+    "build"
+]
+test = [
+    "pytest>=8.2.0",
+    "pytest-xdist>=3.6.1",
+    "pytest-cov>=5.0.0",
+    "nbmake>=1.5.3",
+    "mypy>=1.10.0"
+]
+
+[tool.setuptools]
+package-dir = { "" = "src" }
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-data]
+"*" = ["*.yaml"]
+
+[tool.coverage.run]
+source = ["src/vlab4mic"]
+omit = [
+    "*__init__.py",
+    "*__*.py"
+]
+
+[project.scripts]
+download-structures = "vlab4mic.download:download_suggested_structures"

vlab4mic-0.0.12/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

vlab4mic-0.0.12/src/vlab4mic/__init__.py

@@ -0,0 +1 @@
+from .utils.io.yaml_functions import load_yaml

vlab4mic-0.0.12/src/vlab4mic/analysis/_plots.py

@@ -0,0 +1,108 @@
+import matplotlib.pyplot as plt
+import seaborn as sns
+from ..utils.transform.datatype import truncate
+from matplotlib.ticker import FormatStrFormatter
+
+
+def sns_heatmap_pivots(
+    df_pivots,
+    titles=None,
+    conditions_cmaps=None,
+    annotations=False,
+    cmaps_range="same",
+    figsize=[12, 10],
+    return_figure=False,
+    metric_name=None,
+    decimals="%.4f",
+    fillna = True,
+    **kwargs,
+):
+    conditions = list(df_pivots.keys())
+    nconditions = len(conditions)
+    if "annot_kws" not in kwargs.keys():
+        annot_kws = {"size": 10, "rotation": 45}
+    else:
+        annot_kws = kwargs["annot_kws"]
+    f, axes = plt.subplots(nconditions, 2, figsize=figsize)
+    plot_num = 0
+    if cmaps_range == "same":
+        # min and max here correspond to SSIM
+        hist_params = dict(vmin=0, vmax=1)
+    elif cmaps_range == "each":
+        hist_params = dict()
+    if conditions_cmaps is None:
+        conditions_cmaps = ["mako"] * nconditions
+    if metric_name is not None:
+        metric_n = metric_name
+    else:
+        metric_n = "Metric"
+    for n, cond in enumerate(conditions):
+        if fillna:
+            mask = df_pivots[cond][0].isna()
+            df_pivots[cond][0][mask] = 0.0
+            mask2 = df_pivots[cond][1].isna()
+            df_pivots[cond][1][mask2] = 0.0
+            #print("Na as 0")
+            #print(df_pivots[cond][0])
+        # mean
+        sns.heatmap(
+            df_pivots[cond][0],
+            annot=annotations,
+            annot_kws=annot_kws,
+            ax=axes[n, 0],
+            cmap=conditions_cmaps[n],
+            # xticklabels=df_pivots[cond][0].columns.values.round(3),
+            # yticklabels=df_pivots[cond][0].index.values.round(3),
+            **hist_params,
+            **kwargs
+        )
+        axes[n, 0].set_title(titles["category"] + ": " + cond + ". Mean " + metric_n)
+        #axes[n, 0].yaxis.set_major_formatter(FormatStrFormatter(decimals))
+        #axes[n, 0].xaxis.set_major_formatter(FormatStrFormatter(decimals))
+        # std
+        sns.heatmap(
+            df_pivots[cond][1],
+            annot=annotations,
+            annot_kws=annot_kws,
+            ax=axes[n, 1],
+            cmap=conditions_cmaps[n],
+            # xticklabels=df_pivots[cond][1].columns.values.round(3),
+            # yticklabels=df_pivots[cond][1].index.values.round(3),
+            **kwargs
+        )
+        axes[n, 1].set_title(
+            titles["category"] + ": " + cond + ". Std Dev " + metric_n
+        )
+        #axes[n, 1].yaxis.set_major_formatter(FormatStrFormatter(decimals))
+        #axes[n, 1].xaxis.set_major_formatter(FormatStrFormatter(decimals))
+
+    f.tight_layout()
+
+    if return_figure:
+        plt.close()
+        return f
+
+
+def show_references(references):
+    n_conditions = len(list(references.keys()))
+    f, axes = plt.subplots(1, n_conditions, figsize=(12, 10))
+    i = 0
+    for cond, img in references.items():
+        axes[i].imshow(img, cmap="grey")
+        axes[i].set_title(f"Reference for: {cond}")
+        i = i + 1
+
+
+def show_example_test(
+    queries, params, condition="STED_demo", replica_number=1, query_variant=0
+):  #
+    param_values = [truncate(p, 6) for p in params]
+    print(param_values)
+    combination_pars = [str(val) for val in param_values]
+    print(combination_pars)
+    combination_name = ",".join(combination_pars)
+    print(combination_name)
+    plt.imshow(
+        queries[combination_name][replica_number][condition][query_variant], cmap="grey"
+    )
+    plt.title(combination_name)