Fix frame numbering to be 1-based throughout package (#29)

* Add API overview documentation and functionality

- Introduced `api_overview.md` for comprehensive API documentation.
- Implemented `api.jl` to load and return API overview content.

* Fix frame numbering to be 1-based throughout package

- Change default frame values from 0 to 1 in Emitter2DFit and Emitter3DFit constructors
- Update tests to expect frame=1 as default value
- Update API overview documentation to reflect 1-based frame numbering
- Add CLAUDE.md file for future development guidance
- Frame numbering now follows Julia's 1-based indexing convention

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

* Bump version to 0.3.0 for breaking change in frame numbering

Frame numbering is now 1-based by default, which is a breaking change
from the previous 0-based default. This follows semantic versioning
for breaking changes in the 0.x series.

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

---------

Co-authored-by: Claude <noreply@anthropic.com>

Author: kalidke

CLAUDE.md

@@ -0,0 +1,68 @@
+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Package Overview
+
+SMLMData.jl is a Julia package for handling Single Molecule Localization Microscopy (SMLM) data. It provides types for representing fluorophore localizations, camera geometries, and complete SMLM datasets, along with tools for coordinate conversion, filtering, and I/O operations.
+
+## Development Commands
+
+### Running Tests
+```bash
+# Full test suite
+julia --project=. -e 'using Pkg; Pkg.test()'
+
+# Direct test execution
+julia --project=. test/runtests.jl
+
+# Single test file
+julia --project=. test/test_emitters.jl
+```
+
+### Building Documentation
+```bash
+# Build and open documentation
+julia dev/build_docs.jl
+```
+
+### Package Management
+```bash
+# Install dependencies
+julia --project=. -e 'using Pkg; Pkg.instantiate()'
+
+# Update dependencies
+julia --project=. -e 'using Pkg; Pkg.update()'
+```
+
+## Architecture
+
+### Type Hierarchy
+- **Abstract Types**: `AbstractEmitter`, `AbstractCamera`, `SMLD` define interfaces
+- **Emitter Types**: `Emitter2D`, `Emitter3D`, `Emitter2DFit`, `Emitter3DFit` represent localizations
+- **Container Types**: `BasicSMLD`, `SmiteSMLD` store collections of emitters
+- **Camera Types**: `IdealCamera` defines pixel-to-physical coordinate mapping
+
+### Core Modules
+1. **Coordinates** (`src/core/coordinates.jl`): Conversions between pixel and physical coordinates
+2. **Filters** (`src/core/filters.jl`): `@filter` macro and spatial/temporal selection functions
+3. **Operations** (`src/core/operations.jl`): Dataset concatenation and merging
+4. **I/O** (`src/io/smite/`): SMITE format support for MATLAB interoperability
+
+### Key Design Patterns
+- All spatial coordinates are in microns
+- Parametric types `{T}` for numeric precision flexibility
+- Immutable structs for basic types, mutable for fit results
+- Operations return new SMLD objects (functional style)
+- Macro-based filtering syntax for intuitive API
+
+### Testing Structure
+Tests are organized by component in separate files:
+- `test_emitters.jl`: Emitter type tests
+- `test_cameras.jl`: Camera and coordinate tests
+- `test_smld.jl`: Container type tests
+- `test_filters.jl`: Filtering functionality
+- `test_operations.jl`: Dataset operations
+- `test_smite.jl`: SMITE format I/O
+
+All tests use `@testset` blocks for organization and run via `runtests.jl`.

Project.toml

@@ -1,17 +1,17 @@
-name = "SMLMData"
-uuid = "5488f106-40b8-4660-84c5-84a168990d1b"
-authors = ["klidke@unm.edu"]
-version = "0.2.3"
-
-[deps]
-MAT = "23992714-dd62-5051-b70f-ba57cb901cac"
-
-[compat]
-MAT = "0.10"
-julia = "1.9"
-
-[extras]
-Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
-
-[targets]
-test = ["Test"]
+name = "SMLMData"
+uuid = "5488f106-40b8-4660-84c5-84a168990d1b"
+authors = ["klidke@unm.edu"]
+version = "0.3.0"
+
+[deps]
+MAT = "23992714-dd62-5051-b70f-ba57cb901cac"
+
+[compat]
+MAT = "0.10"
+julia = "1.9"
+
+[extras]
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[targets]
+test = ["Test"]