Update cellfinder CLI name to brainmapper

README.md

@@ -24,15 +24,15 @@ You can also find the documentation for the backend BrainGlobe tools these workf
 
 At present, the package offers the following workflows to users:
 
-- [cellfinder](#cellfinder): a command-line tool for whole-brain detection, registration, and analysis.
+- [brainmapper](#brainmapper-command-line-interface-cli): A command-line tool for whole-brain detection, registration, and analysis.
 
-Additionally, this repository provides functionalities to support code developers. See [Developers documentation](#developers-documentation) for further details.
+Additionally, this repository provides functionalities to support code developers. See the [developer documentation](#developer-documentation) for further details.
 
 ## User documentation
 
+### Installation
 
-### Installation of the cellfinder CLI tool
-At the moment, users can install the cellfinder CLI tool as a standalone tool, by running `pip install` in your desired environment:
+At the moment, users can install all available workflows by running `pip install` in your desired environment:
 
 ```bash
 pip install brainglobe-workflows
@@ -41,43 +41,45 @@ pip install brainglobe-workflows
 `brainglobe-workflows` is built using BrainGlobe tools, and it will automatically fetch the tools that it needs and install them into your environment.
 Once BrainGlobe version 1 is available, this package will fetch all BrainGlobe tools and handle their install into your environment, to prevent potential conflicts from partial-installs.
 
+See the sections below for more information about the workflows and command-line tools provided.
 
-### Cellfinder Command Line Interface (CLI)
+#### `brainmapper` Command Line Interface (CLI)
 
 Whole-brain cell detection, registration and analysis.
 
-If you want to just use the cell detection part of `cellfinder`, please see the standalone [cellfinder](https://github.com/brainglobe/cellfinder-core) package, or the [cellfinder plugin](https://github.com/brainglobe/cellfinder-napari) for [napari](https://napari.org/).
-
+If you want to just use the cell detection part of `brainmapper`, please see the standalone [cellfinder](https://github.com/brainglobe/cellfinder) package and its [`napari`](https://napari.org/) plugin.
 `cellfinder` is a collection of tools developed by [Adam Tyson](https://github.com/adamltyson), [Charly Rousseau](https://github.com/crousseau) and [Christian Niedworok](https://github.com/cniedwor) in the [Margrie Lab](https://www.sainsburywellcome.org/web/groups/margrie-lab), generously supported by the [Sainsbury Wellcome Centre](https://www.sainsburywellcome.org/web/).
 
-`cellfinder` is designed for the analysis of whole-brain imaging data such as [serial-section imaging](https://sainsburywellcomecentre.github.io/OpenSerialSection/) and lightsheet imaging in cleared tissue.
+`brainmapper` is a workflow designed for the analysis of whole-brain imaging data such as [serial-section imaging](https://sainsburywellcomecentre.github.io/OpenSerialSection/) and lightsheet imaging in cleared tissue.
 The aim is to provide a single solution for:
 
-- Cell detection (initial cell candidate detection and refinement using  deep learning) (using the [cellfinder](https://github.com/brainglobe/cellfinder-core) backend package),
+- Cell detection (initial cell candidate detection and refinement using  deep learning) (using the [cellfinder](https://github.com/brainglobe/cellfinder) backend package),
 - Atlas registration (using [brainreg](https://github.com/brainglobe/brainreg)),
 - Analysis of cell positions in a common space.
 
 Basic usage:
 
 ```bash
-cellfinder -s signal_images -b background_images -o output_dir --metadata metadata
+brainmapper -s signal_images -b background_images -o output_dir --metadata metadata
 ```
 
 Full documentation can be found [here](https://brainglobe.info/documentation/cellfinder/index.html).
 
+NOTE: The `brainmapper` workflow previously used the name "cellfinder", but this has been discontinued following the release of the [unified `cellfinder`](https://github.com/brainglobe/cellfinder) backend package to avoid conflation of terms.
+See our [blog post](https://brainglobe.info/blog/version1/cellfinder-core-and-plugin-merge.html) from the release for more information.
 
 ## Developer documentation
 
 This repository also includes workflow scripts that are benchmarked to support code development.
 These benchmarks are run regularly to ensure performance is stable, as the tools are developed and extended.
-* Developers can install these benchmarks locally via `pip install .[dev]`. By executing `asv run`, the benchmarks will run with default parameters on a small dataset that is downloaded from [GIN](https://gin.g-node.org/G-Node/info/wiki). See [the asv docs](https://asv.readthedocs.io/en/v0.6.1/using.html#running-benchmarks) for further details on how to run benchmarks.
-* Developers can also run these benchmarks on data they have stored locally, by specifying the relevant paths in an input (JSON) file.
-* We also maintain an internal runner that benchmarks the workflows over a large, exemplar dataset, of the scale we expect users to be handling. The result of these benchmarks are made publicly available.
+
+- Developers can install these benchmarks locally via `pip install .[dev]`. By executing `asv run`, the benchmarks will run with default parameters on a small dataset that is downloaded from [GIN](https://gin.g-node.org/G-Node/info/wiki). See [the asv docs](https://asv.readthedocs.io/en/v0.6.1/using.html#running-benchmarks) for further details on how to run benchmarks.
+- Developers can also run these benchmarks on data they have stored locally, by specifying the relevant paths in an input (JSON) file.
+- We also maintain an internal runner that benchmarks the workflows over a large, exemplar dataset, of the scale we expect users to be handling. The result of these benchmarks are made publicly available.
 
 Contributions to BrainGlobe are more than welcome.
 Please see the [developer guide](https://brainglobe.info/developers/index.html).
 
-
 ## Citing `brainglobe-workflows`
 
 **If you use any tools in the [brainglobe suite](https://brainglobe.info/documentation/index.html), please [let us know](mailto:[email protected]?subject=cellfinder), and we'd be happy to promote your paper/talk etc.**
@@ -87,5 +89,3 @@ If you find [`cellfinder`](#cellfinder) useful, and use it in your research, ple
 [https://doi.org/10.1371/journal.pcbi.1009074](https://doi.org/10.1371/journal.pcbi.1009074)
 >
 If you use any of the image registration functions in `cellfinder`, please also cite [`brainreg`](https://github.com/brainglobe/brainreg#citing-brainreg).
-
----

brainglobe_workflows/cellfinder_brainreg/analyse/analyse.py → brainglobe_workflows/brainmapper/analyse/analyse.py

@@ -18,7 +18,7 @@
 from brainglobe_utils.general.system import ensure_directory_exists
 from brainglobe_utils.pandas.misc import safe_pandas_concat, sanitise_df
 
-from brainglobe_workflows.cellfinder_brainreg.export.export import (
+from brainglobe_workflows.brainmapper.export.export import (
     export_points,
 )
 

brainglobe_workflows/cellfinder_brainreg/export/export.py → brainglobe_workflows/brainmapper/export/export.py

@@ -1,7 +1,7 @@
-from brainglobe_workflows.cellfinder_brainreg.export.abc4d import (
+from brainglobe_workflows.brainmapper.export.abc4d import (
     export_points as abc4d_export,
 )
-from brainglobe_workflows.cellfinder_brainreg.export.brainrender import (
+from brainglobe_workflows.brainmapper.export.brainrender import (
     export_points as brainrender_export,
 )
 

brainglobe_workflows/cellfinder_brainreg/extract/extract_cubes.py → brainglobe_workflows/brainmapper/extract/extract_cubes.py

@@ -22,10 +22,10 @@
 from tifffile import tifffile
 from tqdm import tqdm
 
-from brainglobe_workflows.cellfinder_brainreg.tools import (
+from brainglobe_workflows.brainmapper.tools import (
     image_processing as img_tools,
 )
-from brainglobe_workflows.cellfinder_brainreg.tools import system
+from brainglobe_workflows.brainmapper.tools import system
 
 
 class StackSizeError(Exception):

brainglobe_workflows/cellfinder_brainreg/figures/figures.py → brainglobe_workflows/brainmapper/figures/figures.py

@@ -1,6 +1,6 @@
 import logging
 
-from brainglobe_workflows.cellfinder_brainreg.figures import heatmap
+from brainglobe_workflows.brainmapper.figures import heatmap
 
 
 def run(args, atlas, downsampled_shape):

brainglobe_workflows/cellfinder_brainreg/main.py → brainglobe_workflows/brainmapper/main.py

@@ -44,7 +44,7 @@ def main():
     suppress_tf_logging(tf_suppress_log_messages)
     from brainreg.core.main import main as register
 
-    from brainglobe_workflows.cellfinder_brainreg.tools import prep
+    from brainglobe_workflows.brainmapper.tools import prep
 
     start_time = datetime.now()
     args, arg_groups, what_to_run, atlas = prep.prep_cellfinder_general()
@@ -105,9 +105,9 @@ def run_all(args, what_to_run, atlas):
     from cellfinder.core.tools import prep
     from cellfinder.core.tools.IO import read_with_dask
 
-    from brainglobe_workflows.cellfinder_brainreg.analyse import analyse
-    from brainglobe_workflows.cellfinder_brainreg.figures import figures
-    from brainglobe_workflows.cellfinder_brainreg.tools.prep import (
+    from brainglobe_workflows.brainmapper.analyse import analyse
+    from brainglobe_workflows.brainmapper.figures import figures
+    from brainglobe_workflows.brainmapper.tools.prep import (
         prep_candidate_detection,
         prep_channel_specific_general,
     )

brainglobe_workflows/cellfinder_brainreg/tools/prep.py → brainglobe_workflows/brainmapper/tools/prep.py

@@ -18,9 +18,9 @@
 from fancylog import fancylog
 
 import brainglobe_workflows as program_for_log
-import brainglobe_workflows.cellfinder_brainreg.tools.parser as parser
-from brainglobe_workflows.cellfinder_brainreg.tools import system, tools
-from brainglobe_workflows.cellfinder_brainreg.tools.parser import (
+import brainglobe_workflows.brainmapper.tools.parser as parser
+from brainglobe_workflows.brainmapper.tools import system, tools
+from brainglobe_workflows.brainmapper.tools.parser import (
     cellfinder_parser,
 )
 

pyproject.toml

@@ -74,7 +74,7 @@ napari = ["napari[pyqt5]", "brainglobe-napari-io", "cellfinder[napari]>=1.0.0"]
 
 [project.scripts]
 cellfinder-workflow = "brainglobe_workflows.cellfinder_core.cellfinder:main_app_wrapper"
-cellfinder = "brainglobe_workflows.cellfinder_brainreg.main:main"
+brainmapper = "brainglobe_workflows.brainmapper.main:main"
 
 [build-system]
 requires = ["setuptools>=45", "wheel", "setuptools_scm[toml]>=6.2"]

tests/cellfinder_brainreg/test_integration/test_detection.py

@@ -6,7 +6,7 @@
 import brainglobe_utils.IO.cells as cell_io
 import pytest
 
-from brainglobe_workflows.cellfinder_brainreg.main import (
+from brainglobe_workflows.brainmapper.main import (
     main as cellfinder_run,
 )
 

tests/cellfinder_brainreg/test_integration/test_extract.py

@@ -12,7 +12,7 @@
 from brainglobe_utils.IO.cells import get_cells
 from tifffile import tifffile
 
-from brainglobe_workflows.cellfinder_brainreg.extract import (
+from brainglobe_workflows.brainmapper.extract import (
     extract_cubes as extract_cubes,
 )
 

tests/cellfinder_brainreg/test_integration/test_registration.py

@@ -7,7 +7,7 @@
 import pytest
 from imio.load import load_any
 
-from brainglobe_workflows.cellfinder_brainreg.main import (
+from brainglobe_workflows.brainmapper.main import (
     main as cellfinder_run,
 )
 

tests/cellfinder_brainreg/test_unit/test_analyse.py

@@ -4,7 +4,7 @@
 
 import pytest
 
-from brainglobe_workflows.cellfinder_brainreg.analyse.analyse import (
+from brainglobe_workflows.brainmapper.analyse.analyse import (
     Point,
     get_region_totals,
 )

tests/cellfinder_brainreg/test_unit/test_tools/test_image_processing.py

@@ -2,7 +2,7 @@
 
 import numpy as np
 
-from brainglobe_workflows.cellfinder_brainreg.tools import (
+from brainglobe_workflows.brainmapper.tools import (
     image_processing as img_tools,
 )
 

tests/cellfinder_brainreg/test_unit/test_tools/test_prep.py

@@ -3,7 +3,7 @@
 import pytest
 from brainglobe_utils.general.exceptions import CommandLineInputError
 
-from brainglobe_workflows.cellfinder_brainreg.tools import prep
+from brainglobe_workflows.brainmapper.tools import prep
 
 # import shutil
 

tests/cellfinder_brainreg/test_unit/test_tools/test_system.py

@@ -6,7 +6,7 @@
 from brainglobe_utils.general.exceptions import CommandLineInputError
 from brainglobe_utils.general.system import ensure_directory_exists
 
-import brainglobe_workflows.cellfinder_brainreg.tools.system as system
+import brainglobe_workflows.brainmapper.tools.system as system
 
 data_dir = Path(__file__).parents[4] / Path("tests", "data")
 background_im_dir = os.path.join(data_dir, "background")

tests/cellfinder_brainreg/test_unit/test_tools/test_tools_general.py

@@ -3,7 +3,7 @@
 import numpy as np
 import pytest
 
-import brainglobe_workflows.cellfinder_brainreg.tools.tools as tools
+import brainglobe_workflows.brainmapper.tools.tools as tools
 
 a = [1, "a", 10, 30]
 b = [30, 10, "c", "d"]