ci-deconvolve 0.1.0__tar.gz

ci_deconvolve-0.1.0/PKG-INFO

@@ -0,0 +1,232 @@
+Metadata-Version: 2.4
+Name: ci-deconvolve
+Version: 0.1.0
+Summary: Focused command-line CI-RL deconvolution for OME-TIFF and OME-Zarr images.
+Author: NL-BioImaging contributors
+License-Expression: MIT
+Keywords: microscopy,deconvolution,ome-tiff,ome-zarr,richardson-lucy
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+Requires-Dist: numpy<3,>=1.26
+Requires-Dist: Pillow>=10.0
+Requires-Dist: tifffile>=2024.1.30
+Requires-Dist: imagecodecs>=2024.1.1
+Requires-Dist: bioio==3.2.0
+Requires-Dist: bioio-ome-tiff==1.4.0
+Requires-Dist: ome-zarr<0.19,>=0.18
+Requires-Dist: numcodecs>=0.14
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: build; extra == "dev"
+Requires-Dist: twine; extra == "dev"
+
+# ci-deconvolve
+
+Focused command-line CI-RL deconvolution for OME-TIFF and OME-Zarr images.
+
+This package installs the `ci_deconvolve` command. On Windows, `pip` also
+creates a `ci_deconvolve.exe` console launcher in the active environment.
+
+## Prerequisite: PyTorch
+
+PyTorch is required but is not bundled in this package. Install the CPU or CUDA
+build that matches your system before running `ci_deconvolve`.
+
+Examples:
+
+```bash
+pip install torch
+```
+
+or install a CUDA build using the command from:
+
+```text
+https://pytorch.org/get-started/locally/
+```
+
+## Install
+
+From this folder during development:
+
+```bash
+pip install -e .
+```
+
+From PyPI after publishing:
+
+```bash
+pip install ci-deconvolve
+```
+
+The package depends on `ome-zarr` for OME-Zarr reading and writing. `zarr` is
+installed transitively by `ome-zarr`; it is not declared as a direct dependency.
+
+## Usage
+
+Run one OME-TIFF file:
+
+```bash
+ci_deconvolve --input image.ome.tiff --output out
+```
+
+Run one OME-Zarr image:
+
+```bash
+ci_deconvolve --input image.ome.zarr --output out --output-format ome-zarr
+```
+
+Run every supported immediate child in a folder:
+
+```bash
+ci_deconvolve --input in_folder --output out_folder --iterations 40
+```
+
+Only these inputs are accepted:
+
+- `.ome.tif`
+- `.ome.tiff`
+- `.zarr` / `.ome.zarr` directories
+
+The CLI always runs `ci_rl`. It intentionally has no `--method` option.
+
+## Examples
+
+```bash
+ci_deconvolve --input image.ome.tiff --output out ^
+  --iterations 40 ^
+  --device auto ^
+  --output-format ome-tiff ^
+  --emission-wl 520 ^
+  --excitation-wl 488 ^
+  --pixel-size-xy 0.065 ^
+  --pixel-size-z 0.2
+```
+
+Use `--overrule-metadata` when CLI metadata values should replace image
+metadata. Without it, CLI metadata values are used as fallbacks.
+
+Per-channel values can be comma-separated. If there are more channels than
+values, the last value is reused for the remaining channels.
+
+```bash
+ci_deconvolve --input image.ome.tiff --output out ^
+  --iterations 40,60,80 ^
+  --emission-wl 520,610 ^
+  --excitation-wl 488,561 ^
+  --pinhole-airy 1.0,1.2
+```
+
+## Parameters
+
+### Required Paths
+
+| Option | Default | Description |
+| --- | --- | --- |
+| `input_path` | none | Optional positional input path. Use this or `--input`. |
+| `--input PATH` | none | Input OME-TIFF file, OME-Zarr folder, or folder containing supported inputs. |
+| `--output DIR` | required | Output folder. Created if it does not exist. |
+
+Supported inputs are immediate files/folders only:
+
+- `.ome.tif`
+- `.ome.tiff`
+- `.zarr` / `.ome.zarr` directories
+
+HCS plate OME-Zarr inputs are detected and rejected clearly; this focused CLI
+does not process plate fields.
+
+### Output And Compute
+
+| Option | Default | Description |
+| --- | --- | --- |
+| `--output-format ome-tiff\|ome-zarr` | `ome-tiff` | Writes `<stem>_decon.ome.tiff` or `<stem>_decon.ome.zarr`. |
+| `--iterations N[,N...]` | `40` | CI-RL iteration count. A comma- or semicolon-separated list applies per channel, with the last value reused for extra channels. |
+| `--device auto\|cpu\|cuda` | `auto` | Compute device. `auto` lets PyTorch choose CUDA when available, otherwise CPU. |
+| `-v`, `--verbose` | off | Enable INFO logging from the CLI and core deconvolution code. |
+
+### CI-RL Solver
+
+| Option | Default | Description |
+| --- | --- | --- |
+| `--background VALUE\|auto` | `auto` | Background level used by the solver. `auto` estimates it from the image. Numeric values are accepted. |
+| `--offset VALUE\|auto\|none` | `auto` | Positive offset added before iteration and removed afterwards. Use `none`, `0`, or `0.0` to disable. |
+| `--damping VALUE\|auto\|none` | `none` | Noise-gated damping strength. Use `auto` for automatic damping, numeric values for manual damping, or `none`/`0` to disable. |
+| `--prefilter-sigma VALUE` | `0.0` | Optional Anscombe/low-pass prefilter sigma. `0.0` disables prefiltering. |
+| `--start MODE` | `auto` | Initial estimate mode. Choices: `auto`, `flat`, `percentile_flat`, `observed`, `observed_bgsub`, `lowpass`, `lowpass_bgsub`, `hybrid`. |
+| `--convergence auto\|fixed\|none` | `auto` | `auto` enables early stopping based on convergence. `fixed` and `none` both run the requested iteration count. |
+| `--rel-threshold VALUE` | `0.005` | Relative convergence threshold used when `--convergence auto`. Values are clamped to at least `1e-8`. |
+| `--check-every N` | `5` | Check convergence every N iterations. Values below 1 are clamped to 1. |
+
+### Metadata And PSF
+
+These values are used to generate the point spread function. By default, image
+metadata wins and CLI values fill in missing metadata. With
+`--overrule-metadata`, CLI values replace image metadata.
+
+| Option | Default | Description |
+| --- | --- | --- |
+| `--na VALUE` | `1.4` | Numerical aperture. |
+| `--refractive-index VALUE` | `1.515` | Immersion medium refractive index, typically oil. |
+| `--sample-ri VALUE` | `1.47` | Sample medium refractive index. |
+| `--microscope-type widefield\|confocal` | `confocal` | Microscope model used for PSF generation. |
+| `--emission-wl VALUE[,VALUE...]` | `520` | Emission wavelength(s), in nm. Per-channel list supported. |
+| `--excitation-wl VALUE[,VALUE...]` | `488` | Excitation wavelength(s), in nm. Per-channel list supported. |
+| `--pinhole-airy VALUE[,VALUE...]` | `1.0` | Confocal pinhole diameter in Airy units. Per-channel list supported. |
+| `--pixel-size-xy VALUE` | `0.065` | Lateral pixel size in micrometers. Applied to X and Y. |
+| `--pixel-size-z VALUE` | `0.2` | Axial pixel size in micrometers. |
+| `--overrule-metadata` | off | Replace image metadata with CLI metadata values instead of only using CLI values as fallbacks. |
+
+List syntax:
+
+```bash
+--emission-wl 520,610
+--excitation-wl 488;561
+--iterations 30,40,50
+```
+
+Commas and semicolons are both accepted.
+
+### 2D Widefield Options
+
+These only affect 2D widefield data when `--microscope-type widefield` and
+`--two-d-mode auto` are used.
+
+| Option | Default | Description |
+| --- | --- | --- |
+| `--two-d-mode auto\|legacy_2d` | `auto` | `auto` enables the enhanced 2D widefield path. `legacy_2d` uses the historical pure-2D PSF behavior. |
+| `--two-d-wf-aggressiveness conservative\|balanced\|strong` | `balanced` | Strength preset for the enhanced 2D widefield model. |
+| `--two-d-wf-bg-radius-um VALUE` | `0.5` | Background-estimation radius in micrometers. Values below `0.1` are clamped to `0.1`. |
+| `--two-d-wf-bg-scale VALUE` | `1.0` | Multiplier for the estimated 2D widefield background. Values below `0.1` are clamped to `0.1`. |
+
+## Metadata Override Behavior
+
+Without `--overrule-metadata`:
+
+- Existing OME metadata is preserved.
+- CLI metadata values are used only when a value is missing or invalid.
+- This is the recommended mode for well-annotated OME-TIFF or OME-Zarr data.
+
+With `--overrule-metadata`:
+
+- CLI metadata values replace image metadata.
+- Use this when source metadata is known to be wrong, incomplete, or converted
+  with incorrect physical pixel sizes or wavelengths.
+
+Example:
+
+```bash
+ci_deconvolve --input image.ome.tiff --output out ^
+  --overrule-metadata ^
+  --microscope-type widefield ^
+  --na 1.40 ^
+  --refractive-index 1.515 ^
+  --sample-ri 1.47 ^
+  --pixel-size-xy 0.065 ^
+  --pixel-size-z 0.200 ^
+  --emission-wl 520,610
+```

ci_deconvolve-0.1.0/README.md

@@ -0,0 +1,205 @@
+# ci-deconvolve
+
+Focused command-line CI-RL deconvolution for OME-TIFF and OME-Zarr images.
+
+This package installs the `ci_deconvolve` command. On Windows, `pip` also
+creates a `ci_deconvolve.exe` console launcher in the active environment.
+
+## Prerequisite: PyTorch
+
+PyTorch is required but is not bundled in this package. Install the CPU or CUDA
+build that matches your system before running `ci_deconvolve`.
+
+Examples:
+
+```bash
+pip install torch
+```
+
+or install a CUDA build using the command from:
+
+```text
+https://pytorch.org/get-started/locally/
+```
+
+## Install
+
+From this folder during development:
+
+```bash
+pip install -e .
+```
+
+From PyPI after publishing:
+
+```bash
+pip install ci-deconvolve
+```
+
+The package depends on `ome-zarr` for OME-Zarr reading and writing. `zarr` is
+installed transitively by `ome-zarr`; it is not declared as a direct dependency.
+
+## Usage
+
+Run one OME-TIFF file:
+
+```bash
+ci_deconvolve --input image.ome.tiff --output out
+```
+
+Run one OME-Zarr image:
+
+```bash
+ci_deconvolve --input image.ome.zarr --output out --output-format ome-zarr
+```
+
+Run every supported immediate child in a folder:
+
+```bash
+ci_deconvolve --input in_folder --output out_folder --iterations 40
+```
+
+Only these inputs are accepted:
+
+- `.ome.tif`
+- `.ome.tiff`
+- `.zarr` / `.ome.zarr` directories
+
+The CLI always runs `ci_rl`. It intentionally has no `--method` option.
+
+## Examples
+
+```bash
+ci_deconvolve --input image.ome.tiff --output out ^
+  --iterations 40 ^
+  --device auto ^
+  --output-format ome-tiff ^
+  --emission-wl 520 ^
+  --excitation-wl 488 ^
+  --pixel-size-xy 0.065 ^
+  --pixel-size-z 0.2
+```
+
+Use `--overrule-metadata` when CLI metadata values should replace image
+metadata. Without it, CLI metadata values are used as fallbacks.
+
+Per-channel values can be comma-separated. If there are more channels than
+values, the last value is reused for the remaining channels.
+
+```bash
+ci_deconvolve --input image.ome.tiff --output out ^
+  --iterations 40,60,80 ^
+  --emission-wl 520,610 ^
+  --excitation-wl 488,561 ^
+  --pinhole-airy 1.0,1.2
+```
+
+## Parameters
+
+### Required Paths
+
+| Option | Default | Description |
+| --- | --- | --- |
+| `input_path` | none | Optional positional input path. Use this or `--input`. |
+| `--input PATH` | none | Input OME-TIFF file, OME-Zarr folder, or folder containing supported inputs. |
+| `--output DIR` | required | Output folder. Created if it does not exist. |
+
+Supported inputs are immediate files/folders only:
+
+- `.ome.tif`
+- `.ome.tiff`
+- `.zarr` / `.ome.zarr` directories
+
+HCS plate OME-Zarr inputs are detected and rejected clearly; this focused CLI
+does not process plate fields.
+
+### Output And Compute
+
+| Option | Default | Description |
+| --- | --- | --- |
+| `--output-format ome-tiff\|ome-zarr` | `ome-tiff` | Writes `<stem>_decon.ome.tiff` or `<stem>_decon.ome.zarr`. |
+| `--iterations N[,N...]` | `40` | CI-RL iteration count. A comma- or semicolon-separated list applies per channel, with the last value reused for extra channels. |
+| `--device auto\|cpu\|cuda` | `auto` | Compute device. `auto` lets PyTorch choose CUDA when available, otherwise CPU. |
+| `-v`, `--verbose` | off | Enable INFO logging from the CLI and core deconvolution code. |
+
+### CI-RL Solver
+
+| Option | Default | Description |
+| --- | --- | --- |
+| `--background VALUE\|auto` | `auto` | Background level used by the solver. `auto` estimates it from the image. Numeric values are accepted. |
+| `--offset VALUE\|auto\|none` | `auto` | Positive offset added before iteration and removed afterwards. Use `none`, `0`, or `0.0` to disable. |
+| `--damping VALUE\|auto\|none` | `none` | Noise-gated damping strength. Use `auto` for automatic damping, numeric values for manual damping, or `none`/`0` to disable. |
+| `--prefilter-sigma VALUE` | `0.0` | Optional Anscombe/low-pass prefilter sigma. `0.0` disables prefiltering. |
+| `--start MODE` | `auto` | Initial estimate mode. Choices: `auto`, `flat`, `percentile_flat`, `observed`, `observed_bgsub`, `lowpass`, `lowpass_bgsub`, `hybrid`. |
+| `--convergence auto\|fixed\|none` | `auto` | `auto` enables early stopping based on convergence. `fixed` and `none` both run the requested iteration count. |
+| `--rel-threshold VALUE` | `0.005` | Relative convergence threshold used when `--convergence auto`. Values are clamped to at least `1e-8`. |
+| `--check-every N` | `5` | Check convergence every N iterations. Values below 1 are clamped to 1. |
+
+### Metadata And PSF
+
+These values are used to generate the point spread function. By default, image
+metadata wins and CLI values fill in missing metadata. With
+`--overrule-metadata`, CLI values replace image metadata.
+
+| Option | Default | Description |
+| --- | --- | --- |
+| `--na VALUE` | `1.4` | Numerical aperture. |
+| `--refractive-index VALUE` | `1.515` | Immersion medium refractive index, typically oil. |
+| `--sample-ri VALUE` | `1.47` | Sample medium refractive index. |
+| `--microscope-type widefield\|confocal` | `confocal` | Microscope model used for PSF generation. |
+| `--emission-wl VALUE[,VALUE...]` | `520` | Emission wavelength(s), in nm. Per-channel list supported. |
+| `--excitation-wl VALUE[,VALUE...]` | `488` | Excitation wavelength(s), in nm. Per-channel list supported. |
+| `--pinhole-airy VALUE[,VALUE...]` | `1.0` | Confocal pinhole diameter in Airy units. Per-channel list supported. |
+| `--pixel-size-xy VALUE` | `0.065` | Lateral pixel size in micrometers. Applied to X and Y. |
+| `--pixel-size-z VALUE` | `0.2` | Axial pixel size in micrometers. |
+| `--overrule-metadata` | off | Replace image metadata with CLI metadata values instead of only using CLI values as fallbacks. |
+
+List syntax:
+
+```bash
+--emission-wl 520,610
+--excitation-wl 488;561
+--iterations 30,40,50
+```
+
+Commas and semicolons are both accepted.
+
+### 2D Widefield Options
+
+These only affect 2D widefield data when `--microscope-type widefield` and
+`--two-d-mode auto` are used.
+
+| Option | Default | Description |
+| --- | --- | --- |
+| `--two-d-mode auto\|legacy_2d` | `auto` | `auto` enables the enhanced 2D widefield path. `legacy_2d` uses the historical pure-2D PSF behavior. |
+| `--two-d-wf-aggressiveness conservative\|balanced\|strong` | `balanced` | Strength preset for the enhanced 2D widefield model. |
+| `--two-d-wf-bg-radius-um VALUE` | `0.5` | Background-estimation radius in micrometers. Values below `0.1` are clamped to `0.1`. |
+| `--two-d-wf-bg-scale VALUE` | `1.0` | Multiplier for the estimated 2D widefield background. Values below `0.1` are clamped to `0.1`. |
+
+## Metadata Override Behavior
+
+Without `--overrule-metadata`:
+
+- Existing OME metadata is preserved.
+- CLI metadata values are used only when a value is missing or invalid.
+- This is the recommended mode for well-annotated OME-TIFF or OME-Zarr data.
+
+With `--overrule-metadata`:
+
+- CLI metadata values replace image metadata.
+- Use this when source metadata is known to be wrong, incomplete, or converted
+  with incorrect physical pixel sizes or wavelengths.
+
+Example:
+
+```bash
+ci_deconvolve --input image.ome.tiff --output out ^
+  --overrule-metadata ^
+  --microscope-type widefield ^
+  --na 1.40 ^
+  --refractive-index 1.515 ^
+  --sample-ri 1.47 ^
+  --pixel-size-xy 0.065 ^
+  --pixel-size-z 0.200 ^
+  --emission-wl 520,610
+```

ci_deconvolve-0.1.0/ci_deconvolve.egg-info/PKG-INFO

@@ -0,0 +1,232 @@
+Metadata-Version: 2.4
+Name: ci-deconvolve
+Version: 0.1.0
+Summary: Focused command-line CI-RL deconvolution for OME-TIFF and OME-Zarr images.
+Author: NL-BioImaging contributors
+License-Expression: MIT
+Keywords: microscopy,deconvolution,ome-tiff,ome-zarr,richardson-lucy
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+Requires-Dist: numpy<3,>=1.26
+Requires-Dist: Pillow>=10.0
+Requires-Dist: tifffile>=2024.1.30
+Requires-Dist: imagecodecs>=2024.1.1
+Requires-Dist: bioio==3.2.0
+Requires-Dist: bioio-ome-tiff==1.4.0
+Requires-Dist: ome-zarr<0.19,>=0.18
+Requires-Dist: numcodecs>=0.14
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: build; extra == "dev"
+Requires-Dist: twine; extra == "dev"
+
+# ci-deconvolve
+
+Focused command-line CI-RL deconvolution for OME-TIFF and OME-Zarr images.
+
+This package installs the `ci_deconvolve` command. On Windows, `pip` also
+creates a `ci_deconvolve.exe` console launcher in the active environment.
+
+## Prerequisite: PyTorch
+
+PyTorch is required but is not bundled in this package. Install the CPU or CUDA
+build that matches your system before running `ci_deconvolve`.
+
+Examples:
+
+```bash
+pip install torch
+```
+
+or install a CUDA build using the command from:
+
+```text
+https://pytorch.org/get-started/locally/
+```
+
+## Install
+
+From this folder during development:
+
+```bash
+pip install -e .
+```
+
+From PyPI after publishing:
+
+```bash
+pip install ci-deconvolve
+```
+
+The package depends on `ome-zarr` for OME-Zarr reading and writing. `zarr` is
+installed transitively by `ome-zarr`; it is not declared as a direct dependency.
+
+## Usage
+
+Run one OME-TIFF file:
+
+```bash
+ci_deconvolve --input image.ome.tiff --output out
+```
+
+Run one OME-Zarr image:
+
+```bash
+ci_deconvolve --input image.ome.zarr --output out --output-format ome-zarr
+```
+
+Run every supported immediate child in a folder:
+
+```bash
+ci_deconvolve --input in_folder --output out_folder --iterations 40
+```
+
+Only these inputs are accepted:
+
+- `.ome.tif`
+- `.ome.tiff`
+- `.zarr` / `.ome.zarr` directories
+
+The CLI always runs `ci_rl`. It intentionally has no `--method` option.
+
+## Examples
+
+```bash
+ci_deconvolve --input image.ome.tiff --output out ^
+  --iterations 40 ^
+  --device auto ^
+  --output-format ome-tiff ^
+  --emission-wl 520 ^
+  --excitation-wl 488 ^
+  --pixel-size-xy 0.065 ^
+  --pixel-size-z 0.2
+```
+
+Use `--overrule-metadata` when CLI metadata values should replace image
+metadata. Without it, CLI metadata values are used as fallbacks.
+
+Per-channel values can be comma-separated. If there are more channels than
+values, the last value is reused for the remaining channels.
+
+```bash
+ci_deconvolve --input image.ome.tiff --output out ^
+  --iterations 40,60,80 ^
+  --emission-wl 520,610 ^
+  --excitation-wl 488,561 ^
+  --pinhole-airy 1.0,1.2
+```
+
+## Parameters
+
+### Required Paths
+
+| Option | Default | Description |
+| --- | --- | --- |
+| `input_path` | none | Optional positional input path. Use this or `--input`. |
+| `--input PATH` | none | Input OME-TIFF file, OME-Zarr folder, or folder containing supported inputs. |
+| `--output DIR` | required | Output folder. Created if it does not exist. |
+
+Supported inputs are immediate files/folders only:
+
+- `.ome.tif`
+- `.ome.tiff`
+- `.zarr` / `.ome.zarr` directories
+
+HCS plate OME-Zarr inputs are detected and rejected clearly; this focused CLI
+does not process plate fields.
+
+### Output And Compute
+
+| Option | Default | Description |
+| --- | --- | --- |
+| `--output-format ome-tiff\|ome-zarr` | `ome-tiff` | Writes `<stem>_decon.ome.tiff` or `<stem>_decon.ome.zarr`. |
+| `--iterations N[,N...]` | `40` | CI-RL iteration count. A comma- or semicolon-separated list applies per channel, with the last value reused for extra channels. |
+| `--device auto\|cpu\|cuda` | `auto` | Compute device. `auto` lets PyTorch choose CUDA when available, otherwise CPU. |
+| `-v`, `--verbose` | off | Enable INFO logging from the CLI and core deconvolution code. |
+
+### CI-RL Solver
+
+| Option | Default | Description |
+| --- | --- | --- |
+| `--background VALUE\|auto` | `auto` | Background level used by the solver. `auto` estimates it from the image. Numeric values are accepted. |
+| `--offset VALUE\|auto\|none` | `auto` | Positive offset added before iteration and removed afterwards. Use `none`, `0`, or `0.0` to disable. |
+| `--damping VALUE\|auto\|none` | `none` | Noise-gated damping strength. Use `auto` for automatic damping, numeric values for manual damping, or `none`/`0` to disable. |
+| `--prefilter-sigma VALUE` | `0.0` | Optional Anscombe/low-pass prefilter sigma. `0.0` disables prefiltering. |
+| `--start MODE` | `auto` | Initial estimate mode. Choices: `auto`, `flat`, `percentile_flat`, `observed`, `observed_bgsub`, `lowpass`, `lowpass_bgsub`, `hybrid`. |
+| `--convergence auto\|fixed\|none` | `auto` | `auto` enables early stopping based on convergence. `fixed` and `none` both run the requested iteration count. |
+| `--rel-threshold VALUE` | `0.005` | Relative convergence threshold used when `--convergence auto`. Values are clamped to at least `1e-8`. |
+| `--check-every N` | `5` | Check convergence every N iterations. Values below 1 are clamped to 1. |
+
+### Metadata And PSF
+
+These values are used to generate the point spread function. By default, image
+metadata wins and CLI values fill in missing metadata. With
+`--overrule-metadata`, CLI values replace image metadata.
+
+| Option | Default | Description |
+| --- | --- | --- |
+| `--na VALUE` | `1.4` | Numerical aperture. |
+| `--refractive-index VALUE` | `1.515` | Immersion medium refractive index, typically oil. |
+| `--sample-ri VALUE` | `1.47` | Sample medium refractive index. |
+| `--microscope-type widefield\|confocal` | `confocal` | Microscope model used for PSF generation. |
+| `--emission-wl VALUE[,VALUE...]` | `520` | Emission wavelength(s), in nm. Per-channel list supported. |
+| `--excitation-wl VALUE[,VALUE...]` | `488` | Excitation wavelength(s), in nm. Per-channel list supported. |
+| `--pinhole-airy VALUE[,VALUE...]` | `1.0` | Confocal pinhole diameter in Airy units. Per-channel list supported. |
+| `--pixel-size-xy VALUE` | `0.065` | Lateral pixel size in micrometers. Applied to X and Y. |
+| `--pixel-size-z VALUE` | `0.2` | Axial pixel size in micrometers. |
+| `--overrule-metadata` | off | Replace image metadata with CLI metadata values instead of only using CLI values as fallbacks. |
+
+List syntax:
+
+```bash
+--emission-wl 520,610
+--excitation-wl 488;561
+--iterations 30,40,50
+```
+
+Commas and semicolons are both accepted.
+
+### 2D Widefield Options
+
+These only affect 2D widefield data when `--microscope-type widefield` and
+`--two-d-mode auto` are used.
+
+| Option | Default | Description |
+| --- | --- | --- |
+| `--two-d-mode auto\|legacy_2d` | `auto` | `auto` enables the enhanced 2D widefield path. `legacy_2d` uses the historical pure-2D PSF behavior. |
+| `--two-d-wf-aggressiveness conservative\|balanced\|strong` | `balanced` | Strength preset for the enhanced 2D widefield model. |
+| `--two-d-wf-bg-radius-um VALUE` | `0.5` | Background-estimation radius in micrometers. Values below `0.1` are clamped to `0.1`. |
+| `--two-d-wf-bg-scale VALUE` | `1.0` | Multiplier for the estimated 2D widefield background. Values below `0.1` are clamped to `0.1`. |
+
+## Metadata Override Behavior
+
+Without `--overrule-metadata`:
+
+- Existing OME metadata is preserved.
+- CLI metadata values are used only when a value is missing or invalid.
+- This is the recommended mode for well-annotated OME-TIFF or OME-Zarr data.
+
+With `--overrule-metadata`:
+
+- CLI metadata values replace image metadata.
+- Use this when source metadata is known to be wrong, incomplete, or converted
+  with incorrect physical pixel sizes or wavelengths.
+
+Example:
+
+```bash
+ci_deconvolve --input image.ome.tiff --output out ^
+  --overrule-metadata ^
+  --microscope-type widefield ^
+  --na 1.40 ^
+  --refractive-index 1.515 ^
+  --sample-ri 1.47 ^
+  --pixel-size-xy 0.065 ^
+  --pixel-size-z 0.200 ^
+  --emission-wl 520,610
+```

ci_deconvolve-0.1.0/ci_deconvolve.egg-info/SOURCES.txt

@@ -0,0 +1,15 @@
+README.md
+pyproject.toml
+ci_deconvolve.egg-info/PKG-INFO
+ci_deconvolve.egg-info/SOURCES.txt
+ci_deconvolve.egg-info/dependency_links.txt
+ci_deconvolve.egg-info/entry_points.txt
+ci_deconvolve.egg-info/requires.txt
+ci_deconvolve.egg-info/top_level.txt
+src/ci_deconvolve/__init__.py
+src/ci_deconvolve/cli.py
+src/core/__init__.py
+src/core/_meta_helpers.py
+src/core/deconvolve.py
+src/core/deconvolve_ci.py
+src/core/ome_zarr_io.py

ci_deconvolve-0.1.0/ci_deconvolve.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

ci_deconvolve-0.1.0/ci_deconvolve.egg-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+ci_deconvolve = ci_deconvolve.cli:main