docs: renamed open-ST to Open-ST

rajewsky-lab · Dec 22, 2023 · 9018de0 · 9018de0
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diff --git a/.github/ISSUE_TEMPLATE/wiki-related.md b/.github/ISSUE_TEMPLATE/wiki-related.md
@@ -1,6 +1,6 @@
 ---
 name: Wiki Issue/Improvement
-about: Report issues or propose improvements for the open-ST wiki
+about: Report issues or propose improvements for the Open-ST wiki
 title: ''
 labels: documentation
 assignees: ''

diff --git a/LICENSE b/LICENSE
@@ -1,6 +1,6 @@
 GNU General Public License, version 2 (GPL-2.0)
 
-openst: computational tools for the analysis of open-ST data.
+openst: computational tools for the analysis of Open-ST data.
 
 Copyright (C) 2023 Daniel León-Periñán, Nikolaos Karaiskos and Nikolaus Rajewsky.
 All rights reserved.

diff --git a/README.md b/README.md
@@ -22,7 +22,7 @@ and includes open-source software for seamless data processing and analysis.
 - Install via `pip install openst`.
 
 ## Tutorials and examples
-We provide [various open-ST datasets](https://openst.github.io/examples) collected by the [Rajewsky lab @ MDC Berlin](https://www.mdc-berlin.de/n-rajewsky), from various tissues/organisms.
+We provide [various Open-ST datasets](https://openst.github.io/examples) collected by the [Rajewsky lab @ MDC Berlin](https://www.mdc-berlin.de/n-rajewsky), from various tissues/organisms.
 There, links to raw and processed data are available, as well as step-by-step guides for (pre)processing and downstream analysis. 
 
 ## Documentation
@@ -59,7 +59,7 @@ In general, you can always refer to the [contribution guidelines](CONTRIBUTING.m
 Currently, only [admins](https://github.com/orgs/rajewsky-lab/people) will be merging all accepted changes.
 
 ## Code of Conduct
-Everyone interacting in the open-ST project's codebases, issue trackers, and discussion forums is expected to follow the [PSF Code of Conduct](https://www.python.org/psf/conduct/).
+Everyone interacting in the Open-ST project's codebases, issue trackers, and discussion forums is expected to follow the [PSF Code of Conduct](https://www.python.org/psf/conduct/).
 
 ## License
 The software tools of this project are under the GNU License - see the [LICENSE](LICENSE) file for details.
diff --git a/docs/computational/generate_expression_matrix.md b/docs/computational/generate_expression_matrix.md
@@ -99,5 +99,5 @@ so it is possible to visualize it with [squidpy](https://github.com/scverse/squi
 among other tools.
 
 So, this concludes the preprocessing of 2D spatial transcriptomics and imaging data
-of the open-ST protocol. Next steps include 3D reconstruction, and
+of the Open-ST protocol. Next steps include 3D reconstruction, and
 downstream analysis of nD data.
diff --git a/docs/computational/getting_started.md b/docs/computational/getting_started.md
@@ -25,7 +25,7 @@ If not, we recommend using [docker].
 
 ### with pip <small>recommended</small>
 
-The computational tools of the open-ST workflow are published as a [Python package]
+The computational tools of the Open-ST workflow are published as a [Python package]
 and can be installed with `pip`, ideally by using a [virtual environment].
 Open up a terminal and install `openst` with:
 

diff --git a/docs/computational/preprocessing_imaging.md b/docs/computational/preprocessing_imaging.md
@@ -10,7 +10,7 @@ image stitching code - runs in any computer, independent of the software provide
 
 !!! warning
      If you use a different microscope, please refer to the documentation of your microscope
-     for how to stitch tile-scans into a single image. The open-ST pipeline expects one single file in either
+     for how to stitch tile-scans into a single image. The Open-ST pipeline expects one single file in either
      `tiff`, `jpeg` or `png` formats.
 
 ## Stitching with the script

diff --git a/docs/computational/preprocessing_sequencing.md b/docs/computational/preprocessing_sequencing.md
@@ -1,9 +1,9 @@
 # Preprocessing sequencing data
 After sequencing, you will get basecall files in `bcl` format, or raw reads in `fastq`
 format (see [sequence file formats](https://www.illumina.com/informatics/sequencing-data-analysis/sequence-file-formats.html)
-from Illumina's website). In the open-ST experimental protocol, there are two points at which
+from Illumina's website). In the Open-ST experimental protocol, there are two points at which
 sequencing is performed: (1) for obtaining the [sequences of the barcoded library](../experimental/capture_area_generation.md#sequencing-of-barcoded-library),
-and (2) for obtaining the [transcriptomic sequences of open-ST library](../experimental/sequencing_of_openst_library.md#sequencing-of-open-st-library).
+and (2) for obtaining the [transcriptomic sequences of Open-ST library](../experimental/sequencing_of_openst_library.md#sequencing-of-Open-ST-library).
 
 We have developed computational tools for processing each of these sequencing rounds.
 By processing (1), you will get a *database* of barcodes and their spatial locations.
@@ -118,14 +118,14 @@ Again, make sure to replace the placeholders (`<...>`). Now, `<bcl_in>` and `<bc
 basecall files are contained and where the converted output `fastq` files will be saved; The rest of
 arguments have the same meaning as above.
 
-## Processing of the open-ST library
+## Processing of the Open-ST library
 The transformation of raw sequencing data into spatially-mapped expression matrices was carried out utilizing 
 [spacemake](https://spacemake.readthedocs.io/en/latest/) (see also in [GitHub](https://github.com/rajewsky-lab/spacemake)), 
 an automated pipeline designed for the preprocessing, alignment, and quantification of single-cell and spatial transcriptomics data.
 
 We refer to the [official documentation](https://spacemake.readthedocs.io/en/latest/) for a complete tutorial on how to install and
 run spacemake. In summary, the user needs to specify a configuration file (by default, we included run modes that are compatible
-with open-ST), and a project configuration, containing the locations to the `fastq` files, to the **spatial barcode coordinate files**
+with Open-ST), and a project configuration, containing the locations to the `fastq` files, to the **spatial barcode coordinate files**
 (generated in the [previous step](#processing-the-sequencing-of-barcoded-library)),
 and other metadata. Then, spacemake automatically processes these data into [h5ad](https://anndata.readthedocs.io/en/latest/fileformat-prose.html)
 files, which basically contain a matrix of barcodes (rows) and genes (columns), with associated metadata and spatial coordinates. 
@@ -138,7 +138,7 @@ The `x_pos` and `y_pos` coordinates from the [table above](#processing-the-seque
 whole extension of the flow cell - which consists of many *tiles* arranged in *lanes* and *swaths*, see above. 
 This manner, we provide code in `openst` and `spacemake` that allows to compute the global coordinates in the 
 case of having a sample whose placement has cover more than one tile
-during the open-ST library preparation. 
+during the Open-ST library preparation. 
 
 When specifying a `run_mode` without meshing and with a `puck_collection`
 (see [spacemake documentation](https://spacemake.readthedocs.io/en/latest/config.html),

diff --git a/docs/examples/e13_brain/preprocessing_sequencing.md b/docs/examples/e13_brain/preprocessing_sequencing.md
@@ -162,4 +162,4 @@ If you specified options for *meshing* in the `run_mode`, there will be a file c
 This contains *approximate* cell-by-gene information, as the transcripts are aggregated by a regular lattice and not by the true spatial arrangement of
 cells. This might be already enough for some analyses. 
 
-Anyway... keep going with the tutorial if you want to unleash the full potential of open-ST 😉.
+Anyway... keep going with the tutorial if you want to unleash the full potential of Open-ST 😉.
diff --git a/docs/examples/getting_started.md b/docs/examples/getting_started.md
@@ -1,7 +1,7 @@
 # Examples
 
 Here you will find several datasets generated in the [Rajewsky lab @ MDC Berlin](https://www.mdc-berlin.de/n-rajewsky)
-leveraging the **open-ST** workflow (experimental and computational).
+leveraging the **Open-ST** workflow (experimental and computational).
 
 ## Datasets
 

diff --git a/docs/experimental/capture_area_generation.md b/docs/experimental/capture_area_generation.md
@@ -1,5 +1,5 @@
 # Capture area generation
-The following section details the generation of capture areas for the open-ST protocol. 
+The following section details the generation of capture areas for the Open-ST protocol. 
 
 By sequencing oligos, which comprise unique 32-nucleotide barcodes, appropriate adapters,
 and a poly-dT, we register the barcode sequences and their associated coordinates on the flow cell.
@@ -75,7 +75,7 @@ to create a database of barcode sequences and their spatial locations.
     Capture areas can be stored dry at -20°C for extended periods of time. We have generated libraries from prepared capture areas stored for 12 months. 
 
 We have designed a cutting guide that facilitates the breaking of the flow cell into regular capture areas. 
-We provide the 3D model of the cutting guide as a printable [stl](../open-ST_cutting_guide_3D_design.stl) file.
+We provide the 3D model of the cutting guide as a printable [stl](../openst_cutting_guide_3D_design.stl) file.
 If you don't have a 3D printer, you can check for [3D printing services near you](https://www.google.com/search?q=3d+printing+service+near+me) -
 they will help you in this endeavor 🤗.
 
@@ -1143,10 +1143,10 @@ Once you have the tool, refer to the video where we explain how to use it:
 ---
 
 :fontawesome-brands-youtube:{ style="color: #EE0F0F" }
-__[open-ST: breaking the flow cell into capture areas]__ by @danilexn – :octicons-clock-24:
+__[Open-ST: breaking the flow cell into capture areas]__ by @danilexn – :octicons-clock-24:
 10m – Learn how to break an Illumina® NovaSeq 6000 S4 flow cell into capture areas 
 using our 3D-printable cutting guide.
 
-  [open-ST: breaking the flow cell into capture areas]: https://www.youtube.com
+  [Open-ST: breaking the flow cell into capture areas]: https://www.youtube.com
 
 ---
diff --git a/docs/experimental/capture_area_generation_with_3d_viewer.ipynb b/docs/experimental/capture_area_generation_with_3d_viewer.ipynb
@@ -5,7 +5,7 @@
    "metadata": {},
    "source": [
     "# Capture area generation\n",
-    "The following section details the generation of capture areas for the open-ST protocol. \n",
+    "The following section details the generation of capture areas for the Open-ST protocol. \n",
     "\n",
     "By sequencing oligos, which comprise unique 32-nucleotide barcodes, appropriate adapters,\n",
     "and a poly-dT, we register the barcode sequences and their associated coordinates on the flow cell.\n",
@@ -80,7 +80,7 @@
     "    Capture areas can be stored dry in the fridge for extended periods of time. We have generated libraries from prepared capture areas stored for x months. \n",
     "\n",
     "We have designed a cutting guide that facilitates the breaking of the flow cell into regular capture areas. \n",
-    "We provide the 3D model of the cutting guide as a printable [stl](../open-ST_cutting_guide_3D_design.stl) file.\n",
+    "We provide the 3D model of the cutting guide as a printable [stl](../Open-ST_cutting_guide_3D_design.stl) file.\n",
     "You can take a look at it in the viewer below."
    ]
   },
@@ -200,7 +200,7 @@
     "from stl import mesh\n",
     "import numpy as np\n",
     "\n",
-    "my_mesh = mesh.Mesh.from_file('/home/dleonpe/data/projects/openst_paper/repos/openst/docs/open-ST_cutting_guide_3D_design.stl')\n",
+    "my_mesh = mesh.Mesh.from_file('/home/dleonpe/data/projects/openst_paper/repos/openst/docs/openst_cutting_guide_3D_design.stl')\n",
     "\n",
     "fig = ipv.figure()\n",
     "n = len(my_mesh.v0)\n",
@@ -235,11 +235,11 @@
     "---\n",
     "\n",
     ":fontawesome-brands-youtube:{ style=\"color: #EE0F0F\" }\n",
-    "__[open-ST: breaking the flow cell into capture areas]__ by @danilexn – :octicons-clock-24:\n",
+    "__[Open-ST: breaking the flow cell into capture areas]__ by @danilexn – :octicons-clock-24:\n",
     "10m – Learn how to break an Illumina® NovaSeq 6000 S4 flow cell into capture areas \n",
     "using our 3D-printable cutting guide.\n",
     "\n",
-    "  [open-ST: breaking the flow cell into capture areas]: https://www.youtube.com\n",
+    "  [Open-ST: breaking the flow cell into capture areas]: https://www.youtube.com\n",
     "\n",
     "---"
    ]

diff --git a/docs/experimental/sequencing_of_openst_library.md b/docs/experimental/sequencing_of_openst_library.md
@@ -1,4 +1,4 @@
-# Sequencing of open-ST library
+# Sequencing of Open-ST library
 
 ## Quantification
 We recommend quantifying your libraries for sequencing using the KAPA Library Quantification Kit.
@@ -22,4 +22,4 @@ Either when using your own sequencing equipment or relying on a sequencing facil
 to (most likely) already [demultiplexed](https://knowledge.illumina.com/software/general/software-general-troubleshooting-list/000005982)
 `fastq` files; otherwise, you can get access to the *raw* basecall files in `bcl` [format](https://support.illumina.com/content/dam/illumina-support/help/Illumina_DRAGEN_Bio_IT_Platform_v3_7_1000000141465/Content/SW/Informatics/Dragen/ToolsiBCL_fDG.htm).
 
-Either of these files shall be used as the input for spacemake [later](../computational/preprocessing_sequencing.md#processing-of-the-open-st-library).
+Either of these files shall be used as the input for spacemake [later](../computational/preprocessing_sequencing.md#processing-of-the-Open-ST-library).
diff --git a/docs/experimental/tissue_processing_and_RNA_qc.md b/docs/experimental/tissue_processing_and_RNA_qc.md
@@ -6,4 +6,4 @@ Test for RNA quality of the OCT-embedded tissue before working with a tissue.
 For this we recommend cutting 5-10 sections of tissue at 10 um thickness. Remove excess OCT as possible and collect the tissue sections in a pre-cooled 1.5 mL tube. Extract total RNA and assess the RNA quality on an automated gel electrophoresis machine, such as the BioAnalyzer or TapeStation. 
 
 Aim for an RNA integrity number (RIN) over 7.
-Samples with lower RIN values can be used for open-ST; however, low RNA integrity negatively impacts library quality.
+Samples with lower RIN values can be used for Open-ST; however, low RNA integrity negatively impacts library quality.
diff --git a/docs/introduction.md b/docs/introduction.md
@@ -1,6 +1,6 @@
-Welcome to openst.bio, where we provide comprehensive resources to help you generate and analyse open-ST data in your lab.
+Welcome to openst.bio, where we provide comprehensive resources to help you generate and analyse Open-ST data in your lab.
 
-Open-ST is a spatial transcriptomics method that enables efficient whole-transcriptome capture at subcellular resolution [Reference, LINK]. We have demonstrated open-ST's wide applicability, showing robust transcriptome capture across various mouse and human tissues. 
+Open-ST is a spatial transcriptomics method that enables efficient whole-transcriptome capture at subcellular resolution [Reference, LINK]. We have demonstrated Open-ST's wide applicability, showing robust transcriptome capture across various mouse and human tissues. 
 Our method is cost-efficient, straightforward to employ, and includes open-source software for seamless data processing and analysis.
 
 Here, you can find detailed step-by-step descriptions of the experimental and the computational workflows. In a FAQ section we address commonly asked questions. Via our [discussion board] you can submit your own questions, and we will do our best to provide answers. 

diff --git a/docs/open-ST_cutting_guide_3D_design.stl → docs/openst_cutting_guide_3D_design.stl b/docs/open-ST_cutting_guide_3D_design.stl → docs/openst_cutting_guide_3D_design.stl
diff --git a/docs/theme_override_home/home.html b/docs/theme_override_home/home.html
@@ -230,7 +230,7 @@
           </video>
         </div>
         <div class="tx-hero__content">
-          <h1><img src="static/logos/openst_logo_transparent_completeO.png" width="60px" style="margin-bottom:-20px"/> <b>open-ST</b> <br><br>Democratizing spatial transcriptomics </h1>
+          <h1><img src="static/logos/openst_logo_transparent_completeO.png" width="60px" style="margin-bottom:-20px"/> <b>Open-ST</b> <br><br>Democratizing spatial transcriptomics </h1>
           <p>An open-source and cheap method with efficient and sub-cellular whole-transcriptome capture.</p>
           <p>  
             <a href="https://pepy.tech/project/openst"><img alt="Downloads" src="https://pepy.tech/badge/openst"></a>
@@ -258,7 +258,7 @@ <h2>
                 <path
                     d="M15 17v-3h3v-2l4 3.5-4 3.5v-2h-3m2 1v3h-3v2l-4-3.5 4-3.5v2h3M12 8c-2.21 0-4 1.8-4 4 0 1.91 1.35 3.54 3.21 3.92L16 11.86A3.997 3.997 0 0012 8m0 6c-1.1 0-2-.89-2-2s.9-2 2-2 2 .9 2 2-.89 2-2 2m9.66-5.27l-2-3.46c-.12-.22-.38-.31-.61-.22l-2.49 1c-.51-.41-1.06-.74-1.69-1l-.37-2.63A.506.506 0 0014 2h-4c-.25 0-.46.18-.5.42l-.37 2.65c-.63.26-1.17.59-1.69 1L5 5.05c-.23-.09-.5 0-.61.22l-2 3.46c-.13.21-.08.49.11.64L4.57 11l-.07 1 .07 1-2.11 1.63c-.2.15-.25.43-.12.64l2 3.46c.11.27.4.38.66.27l2.5-1c.24.19.5.37.76.53l1.65-1.4c-.77-.33-1.45-.82-2-1.45l-2.41 1-.77-1.3L6.8 13.8a5.55 5.55 0 010-3.6L4.69 8.65l.75-1.3 2.41 1c.78-.9 1.83-1.53 3-1.78l.4-2.57h1.5l.37 2.62c1.17.24 2.22.88 3 1.77l2.41-1 .75 1.3-2.08 1.51c.09.26.16.53.2.8h2l2.1-1.63a.48.48 0 00.16-.64M12 8c-2.21 0-4 1.8-4 4 0 1.91 1.35 3.54 3.21 3.92L16 11.86A3.997 3.997 0 0012 8m0 6c-1.1 0-2-.89-2-2s.9-2 2-2 2 .9 2 2-.89 2-2 2m0-6c-2.21 0-4 1.8-4 4 0 1.91 1.35 3.54 3.21 3.92L16 11.86A3.997 3.997 0 0012 8m0 6c-1.1 0-2-.89-2-2s.9-2 2-2 2 .9 2 2-.89 2-2 2z" />
             </svg>
-            open-ST feature A
+            Open-ST feature A
         </h2>
         <p>blah blah blah</p>
     </div>

diff --git a/mkdocs.yml b/mkdocs.yml
@@ -1,10 +1,10 @@
-site_name: open-ST
+site_name: Open-ST
 site_url: https://open.st
 site_author: Daniel León-Periñán, Lena Marie Schott
 site_description: >-
-  open-ST: democratizing spatial transcriptomics 
+  Open-ST: democratizing spatial transcriptomics 
 
-copyright: Copyright &copy; 2023 open-ST
+copyright: Copyright &copy; 2023 Open-ST
 
 repo_name: rajewsky-lab/openst
 repo_url: https://github.com/rajewsky-lab/openst
@@ -18,7 +18,7 @@ nav:
       - Capture area generation: experimental/capture_area_generation.md
       - Tissue processing and RNA quality control: experimental/tissue_processing_and_RNA_qc.md
       - Library preparation: experimental/library_preparation.md
-      - Sequencing of open-ST library: experimental/sequencing_of_openst_library.md
+      - Sequencing of Open-ST library: experimental/sequencing_of_openst_library.md
     - Computational:
       - Getting started: computational/getting_started.md
       - Preprocessing of sequencing: computational/preprocessing_sequencing.md
@@ -78,7 +78,7 @@ plugins:
 - mknotebooks
 
 extra:
-  copyright: Copyright &copy; 2023 open-ST
+  copyright: Copyright &copy; 2023 Open-ST
   social:
     - icon: fontawesome/brands/twitter
       link: https://twitter.com/open_sts

diff --git a/openst/alignment/manual_pairwise_aligner.py b/openst/alignment/manual_pairwise_aligner.py
@@ -131,7 +131,7 @@ def load_keypoints_from_json(fname: str):
     return keypoints_by_key
 
 def _run_manual_pairwise_aligner(args):
-    logging.info("open-ST pairwise alignment; running with parameters:")
+    logging.info("Open-ST pairwise alignment; running with parameters:")
     logging.info(args.__dict__)
 
     # Check input and output data

diff --git a/openst/alignment/manual_pairwise_aligner_gui.py b/openst/alignment/manual_pairwise_aligner_gui.py
@@ -1067,7 +1067,7 @@ def mouseDoubleClickEvent(self, event):
 def _run_manual_pairwise_aligner_gui(*args, **kwargs):
     app = QApplication(sys.argv)
     window = ImageAlignmentApp()
-    window.setWindowTitle("Manual Pairwise Alignment (open-ST)")
+    window.setWindowTitle("Manual Pairwise Alignment (Open-ST)")
     window.setGeometry(100, 100, 1000, 1000)
     window.show()
 

diff --git a/openst/alignment/pairwise_aligner.py b/openst/alignment/pairwise_aligner.py
@@ -1,5 +1,5 @@
 """
-Automatic Pairwise Alignment of Spatial Transcriptomics and Imaging Data (open-ST)
+Automatic Pairwise Alignment of Spatial Transcriptomics and Imaging Data (Open-ST)
 
 Author: Daniel León-Periñán @ N.Rajewsky Lab (BIMSB)
 Date: August 30, 2023
@@ -635,7 +635,7 @@ def src_preprocessor(x, flip, rotation):
 
 
 def run_pairwise_aligner(args):
-    logging.info("open-ST pairwise alignment; running with parameters:")
+    logging.info("Open-ST pairwise alignment; running with parameters:")
     logging.info(args.__dict__)
 
     # Check input and output data

diff --git a/openst/cli.py b/openst/cli.py
@@ -22,7 +22,7 @@
 def cmdline_args():
     parent_parser = argparse.ArgumentParser(
         allow_abbrev=False,
-        description="openst: computational tools of open-ST",
+        description="openst: computational tools of Open-ST",
     )
     parent_parser_subparsers = parent_parser.add_subparsers(help="sub-command help", dest="subcommand")
 

diff --git a/openst/metadata/templates/pairwise_alignment.html b/openst/metadata/templates/pairwise_alignment.html
@@ -1673,7 +1673,7 @@
   <div class="container-fluid main-container">
     <!-- setup 3col/9col grid for toc_float and main content  -->
     <div class="row">
-      <h1><b>open-ST</b> report</h1>
+      <h1><b>Open-ST</b> report</h1>
       <div class="col-xs-12 col-sm-4 col-md-3">
         <div id="TOC" class="tocify">
         </div>

diff --git a/openst/preprocessing/image_preprocess.py b/openst/preprocessing/image_preprocess.py
@@ -15,7 +15,7 @@ def get_image_preprocess_parser():
         argparse.Namespace: Parsed command-line arguments.
     """
     parser = argparse.ArgumentParser(
-        description="preprocess imaging data with CUT model (as in open-ST paper)",
+        description="preprocess imaging data with CUT model (as in Open-ST paper)",
         allow_abbrev=False,
         add_help=False,
     )