spacr 1.0.0__tar.gz → 1.0.5__tar.gz

{spacr-1.0.0/spacr.egg-info → spacr-1.0.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 1.0.0
+Version: 1.0.5
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson
@@ -75,7 +75,7 @@ Requires-Dist: ipywidgets<9.0,>=8.1.2
 Requires-Dist: brokenaxes<1.0,>=0.6.2
 Requires-Dist: huggingface-hub<0.25,>=0.24.0
 Provides-Extra: dev
-Requires-Dist: pytest<3.11,>=3.9; extra == "dev"
+Requires-Dist: pytest<3.12,>=3.9; extra == "dev"
 Provides-Extra: headless
 Requires-Dist: opencv-python-headless; extra == "headless"
 Provides-Extra: full
@@ -91,12 +91,15 @@ Requires-Dist: opencv-python; extra == "full"
    :target: https://github.com/EinarOlafsson/spacr/blob/main/LICENSE
 .. |repo size| image:: https://img.shields.io/github/repo-size/EinarOlafsson/spacr
    :target: https://github.com/EinarOlafsson/spacr/
+.. |Tutorial| image:: https://img.shields.io/badge/Tutorial-Click%20Here-brightgreen
+   :target: https://einarolafsson.github.io/spacr/tutorial/
+
 
 .. _docs: https://einarolafsson.github.io/spacr/index.html
 
 Badges
 ------
-|Docs| |PyPI version| |Python version| |Licence: MIT| |repo size|
+|Docs| |PyPI version| |Python version| |Licence: MIT| |repo size| |Tutorial|
 
 SpaCr
 =====
@@ -123,7 +126,6 @@ Features
    :alt: SpaCr workflow
    :align: center
 
-
 **Overview and data organization of spaCR.**
 
 **a.** Schematic workflow of the spaCR pipeline for pooled image-based CRISPR screens. Microscopy images (TIFF, LIF, CZI, NDI) and sequencing reads (FASTQ) are used as inputs (black). The main modules (teal) are: (1) Mask: generates object masks for cells, nuclei, pathogens, and cytoplasm; (2) Measure: extracts object-level features and crops object images, storing quantitative data in an SQL database; (3) Classify—applies machine learning (ML, e.g., XGBoost) or deep learning (DL, e.g., PyTorch) models to classify objects, summarizing results as well-level classification scores; (4) Map Barcodes: extracts and maps row, column, and gRNA barcodes from sequencing data to corresponding wells; (5) Regression: estimates gRNA effect sizes and gene scores via multiple linear regression using well-level summary statistics.
@@ -141,8 +143,7 @@ If using Windows, switch to Linux—it's free, open-source, and better.
 
 ::
 
-   brew install libomp
-   brew install hdf5
+   brew install libomp hdf5 cmake openssl
 
 **Linux GUI requirement:**  
 SpaCr GUI requires Tkinter.  
@@ -163,16 +164,6 @@ SpaCr GUI requires Tkinter.
 
    spacr
 
-Data Availability
------------------
-
-- **Raw sequencing data** are available from NCBI BioProject `PRJNA1261935 <https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1261935>`_ and SRA accessions: `SRR33531217 <https://www.ncbi.nlm.nih.gov/sra/SRR33531217>`_, `SRR33531218 <https://www.ncbi.nlm.nih.gov/sra/SRR33531218>`_, `SRR33531219 <https://www.ncbi.nlm.nih.gov/sra/SRR33531219>`_, `SRR33531220 <https://www.ncbi.nlm.nih.gov/sra/SRR33531220>`_
-
-- **Image data** is deposited at EBI BioStudies under accession: 
-  `S-BIAD2076 <https://www.ebi.ac.uk/biostudies/studies/S-BIAD2076>`_  
-  *(If the link redirects to the main BioStudies portal, copy and paste it directly into your browser.)*
-
-
 Example Notebooks
 -----------------
 
@@ -201,7 +192,26 @@ Interactive Tutorial (under construction)
 
 Click below to explore the step-by-step GUI and Notebook tutorials for spaCR:
 
-`spaCR Tutorial Page <https://einarolafsson.github.io/spacr/tutorial/>`_
+|Tutorial|
+
+spaCRPower
+----------
+
+Power analasys of pooled perterbation spaCR screens.
+
+`spaCRPower <https://github.com/maomlab/spaCRPower>`_
+
+Data Availability
+-----------------
+
+- **Full microscopy image dataset:**  
+  `EMBL-EBI BioStudies S-BIAD2135 <https://doi.org/10.6019/S-BIAD2135>`_
+
+- **Testing dataset:**  
+  `Hugging Face toxo_mito <https://huggingface.co/datasets/einarolafsson/toxo_mito>`_
+
+- **Sequencing data:**  
+  `NCBI BioProject PRJNA1261935 <https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA1261935>`_
 
 License
 -------
@@ -213,3 +223,10 @@ How to Cite
 If you use spaCR in your research, please cite:  
 Olafsson EB, et al. SpaCr: Spatial phenotype analysis of CRISPR-Cas9 screens. *Manuscript in preparation*.
 
+Papers Using spaCR
+-------------------
+Below are selected publications that have used or cited spaCR:
+
+- Olafsson EB, et al. *SpaCr: Spatial phenotype analysis of CRISPR-Cas9 screens.* Manuscript in preparation.
+- `IRE1α promotes phagosomal calcium flux to enhance macrophage fungicidal activity  <https://doi.org/10.1016/j.celrep.2025.115694>`_
+- `Metabolic adaptability and nutrient scavenging in Toxoplasma gondii: insights from ingestion pathway-deficient mutants  <https://doi.org/10.1128/msphere.01011-24>`_

{spacr-1.0.0 → spacr-1.0.5}/README.rst

@@ -8,12 +8,15 @@
    :target: https://github.com/EinarOlafsson/spacr/blob/main/LICENSE
 .. |repo size| image:: https://img.shields.io/github/repo-size/EinarOlafsson/spacr
    :target: https://github.com/EinarOlafsson/spacr/
+.. |Tutorial| image:: https://img.shields.io/badge/Tutorial-Click%20Here-brightgreen
+   :target: https://einarolafsson.github.io/spacr/tutorial/
+
 
 .. _docs: https://einarolafsson.github.io/spacr/index.html
 
 Badges
 ------
-|Docs| |PyPI version| |Python version| |Licence: MIT| |repo size|
+|Docs| |PyPI version| |Python version| |Licence: MIT| |repo size| |Tutorial|
 
 SpaCr
 =====
@@ -40,7 +43,6 @@ Features
    :alt: SpaCr workflow
    :align: center
 
-
 **Overview and data organization of spaCR.**
 
 **a.** Schematic workflow of the spaCR pipeline for pooled image-based CRISPR screens. Microscopy images (TIFF, LIF, CZI, NDI) and sequencing reads (FASTQ) are used as inputs (black). The main modules (teal) are: (1) Mask: generates object masks for cells, nuclei, pathogens, and cytoplasm; (2) Measure: extracts object-level features and crops object images, storing quantitative data in an SQL database; (3) Classify—applies machine learning (ML, e.g., XGBoost) or deep learning (DL, e.g., PyTorch) models to classify objects, summarizing results as well-level classification scores; (4) Map Barcodes: extracts and maps row, column, and gRNA barcodes from sequencing data to corresponding wells; (5) Regression: estimates gRNA effect sizes and gene scores via multiple linear regression using well-level summary statistics.
@@ -58,8 +60,7 @@ If using Windows, switch to Linux—it's free, open-source, and better.
 
 ::
 
-   brew install libomp
-   brew install hdf5
+   brew install libomp hdf5 cmake openssl
 
 **Linux GUI requirement:**  
 SpaCr GUI requires Tkinter.  
@@ -80,16 +81,6 @@ SpaCr GUI requires Tkinter.
 
    spacr
 
-Data Availability
------------------
-
-- **Raw sequencing data** are available from NCBI BioProject `PRJNA1261935 <https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1261935>`_ and SRA accessions: `SRR33531217 <https://www.ncbi.nlm.nih.gov/sra/SRR33531217>`_, `SRR33531218 <https://www.ncbi.nlm.nih.gov/sra/SRR33531218>`_, `SRR33531219 <https://www.ncbi.nlm.nih.gov/sra/SRR33531219>`_, `SRR33531220 <https://www.ncbi.nlm.nih.gov/sra/SRR33531220>`_
-
-- **Image data** is deposited at EBI BioStudies under accession: 
-  `S-BIAD2076 <https://www.ebi.ac.uk/biostudies/studies/S-BIAD2076>`_  
-  *(If the link redirects to the main BioStudies portal, copy and paste it directly into your browser.)*
-
-
 Example Notebooks
 -----------------
 
@@ -118,7 +109,26 @@ Interactive Tutorial (under construction)
 
 Click below to explore the step-by-step GUI and Notebook tutorials for spaCR:
 
-`spaCR Tutorial Page <https://einarolafsson.github.io/spacr/tutorial/>`_
+|Tutorial|
+
+spaCRPower
+----------
+
+Power analasys of pooled perterbation spaCR screens.
+
+`spaCRPower <https://github.com/maomlab/spaCRPower>`_
+
+Data Availability
+-----------------
+
+- **Full microscopy image dataset:**  
+  `EMBL-EBI BioStudies S-BIAD2135 <https://doi.org/10.6019/S-BIAD2135>`_
+
+- **Testing dataset:**  
+  `Hugging Face toxo_mito <https://huggingface.co/datasets/einarolafsson/toxo_mito>`_
+
+- **Sequencing data:**  
+  `NCBI BioProject PRJNA1261935 <https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA1261935>`_
 
 License
 -------
@@ -130,3 +140,10 @@ How to Cite
 If you use spaCR in your research, please cite:  
 Olafsson EB, et al. SpaCr: Spatial phenotype analysis of CRISPR-Cas9 screens. *Manuscript in preparation*.
 
+Papers Using spaCR
+-------------------
+Below are selected publications that have used or cited spaCR:
+
+- Olafsson EB, et al. *SpaCr: Spatial phenotype analysis of CRISPR-Cas9 screens.* Manuscript in preparation.
+- `IRE1α promotes phagosomal calcium flux to enhance macrophage fungicidal activity  <https://doi.org/10.1016/j.celrep.2025.115694>`_
+- `Metabolic adaptability and nutrient scavenging in Toxoplasma gondii: insights from ingestion pathway-deficient mutants  <https://doi.org/10.1128/msphere.01011-24>`_

spacr-1.0.5/docs/_build/html/_modules/index.html

@@ -0,0 +1,166 @@
+
+
+<!DOCTYPE html>
+<html class="writer-html5" lang="en" data-content_root="../">
+<head>
+  <meta charset="utf-8" />
+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  <title>Overview: module code &mdash; spacr 1.0.1 documentation</title>
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=80d5e7a1" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=e59714d7" />
+      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=fd3f3429" />
+      <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=45a07ac9" />
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+      <script src="../_static/jquery.js?v=5d32c60e"></script>
+      <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+      <script src="../_static/documentation_options.js?v=292eb321"></script>
+      <script src="../_static/doctools.js?v=9a2dae69"></script>
+      <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+    <script src="../_static/js/theme.js"></script>
+    <link rel="index" title="Index" href="../genindex.html" />
+    <link rel="search" title="Search" href="../search.html" /> 
+</head>
+
+<body class="wy-body-for-nav"> 
+  <div class="wy-grid-for-nav">
+    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+      <div class="wy-side-scroll">
+        <div class="wy-side-nav-search"  style="background: #005f73" >
+
+          
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+          <a href="../index.html">
+            
+              <img src="../_static/logo_spacr.png" class="logo" alt="Logo"/>
+          </a>
+<div role="search">
+  <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
+    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
+    <input type="hidden" name="check_keywords" value="yes" />
+    <input type="hidden" name="area" value="default" />
+  </form>
+</div>
+        </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="../api/index.html">API Reference</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="../api/spacr/index.html">spacr</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="../api/spacr/index.html#submodules">Submodules</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/app_annotate/index.html">spacr.app_annotate</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/app_classify/index.html">spacr.app_classify</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/app_make_masks/index.html">spacr.app_make_masks</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/app_mask/index.html">spacr.app_mask</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/app_measure/index.html">spacr.app_measure</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/app_sequencing/index.html">spacr.app_sequencing</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/app_umap/index.html">spacr.app_umap</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/core/index.html">spacr.core</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/deep_spacr/index.html">spacr.deep_spacr</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/gui/index.html">spacr.gui</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/gui_core/index.html">spacr.gui_core</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/gui_elements/index.html">spacr.gui_elements</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/gui_utils/index.html">spacr.gui_utils</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/io/index.html">spacr.io</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/logger/index.html">spacr.logger</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/measure/index.html">spacr.measure</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/ml/index.html">spacr.ml</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/plot/index.html">spacr.plot</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/sequencing/index.html">spacr.sequencing</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/settings/index.html">spacr.settings</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/sim/index.html">spacr.sim</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/sp_stats/index.html">spacr.sp_stats</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/spacr_cellpose/index.html">spacr.spacr_cellpose</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/submodules/index.html">spacr.submodules</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/timelapse/index.html">spacr.timelapse</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/toxo/index.html">spacr.toxo</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/utils/index.html">spacr.utils</a></li>
+<li class="toctree-l4"><a class="reference internal" href="../api/spacr/version/index.html">spacr.version</a></li>
+</ul>
+</li>
+</ul>
+</li>
+</ul>
+</li>
+</ul>
+
+        </div>
+      </div>
+    </nav>
+
+    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu"  style="background: #005f73" >
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+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+             
+  <h1>All modules for which code is available</h1>
+<ul><li><a href="spacr/app_annotate.html">spacr.app_annotate</a></li>
+<li><a href="spacr/app_classify.html">spacr.app_classify</a></li>
+<li><a href="spacr/app_make_masks.html">spacr.app_make_masks</a></li>
+<li><a href="spacr/app_mask.html">spacr.app_mask</a></li>
+<li><a href="spacr/app_measure.html">spacr.app_measure</a></li>
+<li><a href="spacr/app_sequencing.html">spacr.app_sequencing</a></li>
+<li><a href="spacr/app_umap.html">spacr.app_umap</a></li>
+<li><a href="spacr/core.html">spacr.core</a></li>
+<li><a href="spacr/deep_spacr.html">spacr.deep_spacr</a></li>
+<li><a href="spacr/gui.html">spacr.gui</a></li>
+<li><a href="spacr/gui_core.html">spacr.gui_core</a></li>
+<li><a href="spacr/gui_elements.html">spacr.gui_elements</a></li>
+<li><a href="spacr/gui_utils.html">spacr.gui_utils</a></li>
+<li><a href="spacr/io.html">spacr.io</a></li>
+<li><a href="spacr/logger.html">spacr.logger</a></li>
+<li><a href="spacr/measure.html">spacr.measure</a></li>
+<li><a href="spacr/ml.html">spacr.ml</a></li>
+<li><a href="spacr/plot.html">spacr.plot</a></li>
+<li><a href="spacr/sequencing.html">spacr.sequencing</a></li>
+<li><a href="spacr/settings.html">spacr.settings</a></li>
+<li><a href="spacr/sim.html">spacr.sim</a></li>
+<li><a href="spacr/sp_stats.html">spacr.sp_stats</a></li>
+<li><a href="spacr/spacr_cellpose.html">spacr.spacr_cellpose</a></li>
+<li><a href="spacr/submodules.html">spacr.submodules</a></li>
+<li><a href="spacr/timelapse.html">spacr.timelapse</a></li>
+<li><a href="spacr/toxo.html">spacr.toxo</a></li>
+<li><a href="spacr/utils.html">spacr.utils</a></li>
+<li><a href="spacr/version.html">spacr.version</a></li>
+</ul>
+
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{spacr-1.0.0/docs → spacr-1.0.5/docs/_build/html}/_modules/spacr/app_annotate.html

@@ -5,14 +5,16 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>spacr.app_annotate &mdash; spacr 0.5.0 documentation</title>
+  <title>spacr.app_annotate &mdash; spacr 1.0.1 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=80d5e7a1" />
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       <link rel="stylesheet" type="text/css" href="../../_static/graphviz.css?v=fd3f3429" />
-      <link rel="stylesheet" type="text/css" href="../../_static/custom.css" />
+      <link rel="stylesheet" type="text/css" href="../../_static/custom.css?v=45a07ac9" />
 
   
-      <script src="../../_static/documentation_options.js?v=1dd76d02"></script>
+      <script src="../../_static/jquery.js?v=5d32c60e"></script>
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@@ -42,27 +44,6 @@
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-<li class="toctree-l4"><a class="reference internal" href="../../api/main/index.html#main.main"><code class="docutils literal notranslate"><span class="pre">main()</span></code></a></li>
-<li class="toctree-l4"><a class="reference internal" href="../../api/main/index.html#main.parser"><code class="docutils literal notranslate"><span class="pre">parser</span></code></a></li>
-<li class="toctree-l4"><a class="reference internal" href="../../api/main/index.html#main.args"><code class="docutils literal notranslate"><span class="pre">args</span></code></a></li>
-<li class="toctree-l4"><a class="reference internal" href="../../api/main/index.html#main.opt"><code class="docutils literal notranslate"><span class="pre">opt</span></code></a></li>
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-<li class="toctree-l4"><a class="reference internal" href="../../api/core/BaseTrainer/index.html">core.BaseTrainer</a></li>
-<li class="toctree-l4"><a class="reference internal" href="../../api/core/Baseline/index.html">core.Baseline</a></li>
-<li class="toctree-l4"><a class="reference internal" href="../../api/core/MEDIAR/index.html">core.MEDIAR</a></li>
-<li class="toctree-l4"><a class="reference internal" href="../../api/core/utils/index.html">core.utils</a></li>
-</ul>
-</li>
-</ul>
-</li>
 <li class="toctree-l2"><a class="reference internal" href="../../api/spacr/index.html">spacr</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="../../api/spacr/index.html#submodules">Submodules</a><ul>
 <li class="toctree-l4"><a class="reference internal" href="../../api/spacr/app_annotate/index.html">spacr.app_annotate</a></li>
@@ -72,7 +53,6 @@
 <li class="toctree-l4"><a class="reference internal" href="../../api/spacr/app_measure/index.html">spacr.app_measure</a></li>
 <li class="toctree-l4"><a class="reference internal" href="../../api/spacr/app_sequencing/index.html">spacr.app_sequencing</a></li>
 <li class="toctree-l4"><a class="reference internal" href="../../api/spacr/app_umap/index.html">spacr.app_umap</a></li>
-<li class="toctree-l4"><a class="reference internal" href="../../api/spacr/chat_bot/index.html">spacr.chat_bot</a></li>
 <li class="toctree-l4"><a class="reference internal" href="../../api/spacr/core/index.html">spacr.core</a></li>
 <li class="toctree-l4"><a class="reference internal" href="../../api/spacr/deep_spacr/index.html">spacr.deep_spacr</a></li>
 <li class="toctree-l4"><a class="reference internal" href="../../api/spacr/gui/index.html">spacr.gui</a></li>
@@ -82,9 +62,7 @@
 <li class="toctree-l4"><a class="reference internal" href="../../api/spacr/io/index.html">spacr.io</a></li>
 <li class="toctree-l4"><a class="reference internal" href="../../api/spacr/logger/index.html">spacr.logger</a></li>
 <li class="toctree-l4"><a class="reference internal" href="../../api/spacr/measure/index.html">spacr.measure</a></li>
-<li class="toctree-l4"><a class="reference internal" href="../../api/spacr/mediar/index.html">spacr.mediar</a></li>
 <li class="toctree-l4"><a class="reference internal" href="../../api/spacr/ml/index.html">spacr.ml</a></li>
-<li class="toctree-l4"><a class="reference internal" href="../../api/spacr/openai/index.html">spacr.openai</a></li>
 <li class="toctree-l4"><a class="reference internal" href="../../api/spacr/plot/index.html">spacr.plot</a></li>
 <li class="toctree-l4"><a class="reference internal" href="../../api/spacr/sequencing/index.html">spacr.sequencing</a></li>
 <li class="toctree-l4"><a class="reference internal" href="../../api/spacr/settings/index.html">spacr.settings</a></li>
@@ -100,53 +78,6 @@
 </li>
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="../../api/predict/index.html">predict</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="../../api/predict/index.html#module-contents">Module Contents</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="../../api/predict/index.html#predict.main"><code class="docutils literal notranslate"><span class="pre">main()</span></code></a></li>
-<li class="toctree-l4"><a class="reference internal" href="../../api/predict/index.html#predict.parser"><code class="docutils literal notranslate"><span class="pre">parser</span></code></a></li>
-<li class="toctree-l4"><a class="reference internal" href="../../api/predict/index.html#predict.args"><code class="docutils literal notranslate"><span class="pre">args</span></code></a></li>
-<li class="toctree-l4"><a class="reference internal" href="../../api/predict/index.html#predict.opt"><code class="docutils literal notranslate"><span class="pre">opt</span></code></a></li>
-</ul>
-</li>
-</ul>
-</li>
-<li class="toctree-l2"><a class="reference internal" href="../../api/evaluate/index.html">evaluate</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="../../api/evaluate/index.html#module-contents">Module Contents</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="../../api/evaluate/index.html#evaluate.main"><code class="docutils literal notranslate"><span class="pre">main()</span></code></a></li>
-</ul>
-</li>
-</ul>
-</li>
-<li class="toctree-l2"><a class="reference internal" href="../../api/SetupDict/index.html">SetupDict</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="../../api/SetupDict/index.html#module-contents">Module Contents</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="../../api/SetupDict/index.html#SetupDict.TRAINER"><code class="docutils literal notranslate"><span class="pre">TRAINER</span></code></a></li>
-<li class="toctree-l4"><a class="reference internal" href="../../api/SetupDict/index.html#SetupDict.OPTIMIZER"><code class="docutils literal notranslate"><span class="pre">OPTIMIZER</span></code></a></li>
-<li class="toctree-l4"><a class="reference internal" href="../../api/SetupDict/index.html#SetupDict.SCHEDULER"><code class="docutils literal notranslate"><span class="pre">SCHEDULER</span></code></a></li>
-</ul>
-</li>
-</ul>
-</li>
-<li class="toctree-l2"><a class="reference internal" href="../../api/train_tools/index.html">train_tools</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="../../api/train_tools/index.html#submodules">Submodules</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="../../api/train_tools/data_utils/index.html">train_tools.data_utils</a></li>
-<li class="toctree-l4"><a class="reference internal" href="../../api/train_tools/measures/index.html">train_tools.measures</a></li>
-<li class="toctree-l4"><a class="reference internal" href="../../api/train_tools/models/index.html">train_tools.models</a></li>
-<li class="toctree-l4"><a class="reference internal" href="../../api/train_tools/utils/index.html">train_tools.utils</a></li>
-</ul>
-</li>
-</ul>
-</li>
-<li class="toctree-l2"><a class="reference internal" href="../../api/generate_mapping/index.html">generate_mapping</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="../../api/generate_mapping/index.html#module-contents">Module Contents</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="../../api/generate_mapping/index.html#generate_mapping.public_paths_labeled"><code class="docutils literal notranslate"><span class="pre">public_paths_labeled()</span></code></a></li>
-<li class="toctree-l4"><a class="reference internal" href="../../api/generate_mapping/index.html#generate_mapping.official_paths_labeled"><code class="docutils literal notranslate"><span class="pre">official_paths_labeled()</span></code></a></li>
-<li class="toctree-l4"><a class="reference internal" href="../../api/generate_mapping/index.html#generate_mapping.official_paths_tuning"><code class="docutils literal notranslate"><span class="pre">official_paths_tuning()</span></code></a></li>
-<li class="toctree-l4"><a class="reference internal" href="../../api/generate_mapping/index.html#generate_mapping.add_mapping_to_json"><code class="docutils literal notranslate"><span class="pre">add_mapping_to_json()</span></code></a></li>
-<li class="toctree-l4"><a class="reference internal" href="../../api/generate_mapping/index.html#generate_mapping.parser"><code class="docutils literal notranslate"><span class="pre">parser</span></code></a></li>
-</ul>
-</li>
-</ul>
-</li>
 </ul>
 </li>
 </ul>
@@ -213,6 +144,10 @@
         <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;percentiles&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="n">convert_to_number</span><span class="p">,</span> <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;percentiles&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)))</span> <span class="k">if</span> <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;percentiles&#39;</span><span class="p">]</span> <span class="k">else</span> <span class="p">[</span><span class="mi">2</span><span class="p">,</span> <span class="mi">98</span><span class="p">]</span>
         <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;normalize&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;normalize&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="s1">&#39;true&#39;</span>
         <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;normalize_channels&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;normalize_channels&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)</span>
+        <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;outline&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;outline&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)</span> <span class="k">if</span> <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;outline&#39;</span><span class="p">]</span> <span class="k">else</span> <span class="kc">None</span>
+        <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;outline_threshold_factor&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">settings</span><span class="p">[</span><span class="s1">&#39;outline_threshold_factor&#39;</span><span class="p">])</span> <span class="k">if</span> <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;outline_threshold_factor&#39;</span><span class="p">]</span> <span class="k">else</span> <span class="mf">1.0</span>
+        <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;outline_sigma&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">settings</span><span class="p">[</span><span class="s1">&#39;outline_threshold_factor&#39;</span><span class="p">])</span> <span class="k">if</span> <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;outline_threshold_factor&#39;</span><span class="p">]</span> <span class="k">else</span> <span class="mf">1.0</span>
+        
         <span class="k">try</span><span class="p">:</span>
             <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;measurement&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;measurement&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)</span> <span class="k">if</span> <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;measurement&#39;</span><span class="p">]</span> <span class="k">else</span> <span class="kc">None</span>
             <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;threshold&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span> <span class="k">if</span> <span class="n">settings</span><span class="p">[</span><span class="s1">&#39;threshold&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="s1">&#39;none&#39;</span> <span class="k">else</span> <span class="nb">int</span><span class="p">(</span><span class="n">settings</span><span class="p">[</span><span class="s1">&#39;threshold&#39;</span><span class="p">])</span>