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+# automatic target selection widget
+
+## Introduction
+
+Previously, selecting the appropriate region of the atlas (i.e. the slice or
+sub-volume to use as a registration target) was a **manual process**. Users
+would visually scroll through atlas slices, estimate where their sample
+belonged, and manually input corresponding rotation angles.
+
+This process could be time-consuming and error-prone - especially when
+working with noisy or partial data.
+
+`automated_target_selection` enables **automatic atlas target selection**, 
+integrated directly into the [brainglobe-registration](https://github.com/brainglobe/brainglobe-registration) 
+Napari plugin.
+
+## Details
+
+The new `automated_target_selection` widget allows users to automatically 
+determine the **best-matching slice and rotation parameters** (pitch, yaw, 
+roll) of a [brainglobe-atlasapi](https://github.com/brainglobe/brainglobe-atlasapi) 
+atlas for a given 2D sample image.
+
+This serves as a pre-processing step before full registration and removes the 
+guesswork from target selection.
+
+The widget uses [Bayesian Optimisation](https://github.com/bayesian-optimization/BayesianOptimization) 
+to iteratively find the atlas slice and orientation that maximises image 
+similarity between your sample and candidate atlas slices.
+
+## How to install
+
+The widget is included in the latest version of `brainglobe-registration`.
+You can install `brainglobe-registration` via [pip](https://pypi.org/project/pip/):
+
+```
+pip install brainglobe-registration
+```
+If already installed, upgrade to the latest version:
+```
+pip install brainglobe-registration --upgrade
+```
+
+Or install [via napari](https://napari.org/stable/plugins/start_using_plugins/finding_and_installing_plugins.html).
+
+## How to use
+
+After scaling your image in the *Prepare Images* section of the plugin, you 
+can open the **Automatic Slice Detection** dialog. You can then define a few 
+key parameters:
+
+![img_1.png](img_1.png)
+
+### 1. Z range
+
+Use the Napari z-slider to estimate a rough region of the atlas that your 
+sample might correspond to - e.g. slices 50 to 80. The optimisation will only 
+search within this range.
+
+If you are unsure, you can use the full atlas range (which is set by default).
+
+### 2. Pitch / yaw / roll bounds (in degrees)
+
+Rotation parameters help match the orientation of your sample to the atlas.
+
+- **Pitch:** rotation around the **left-right** axis.
+- **Yaw:** rotation around the **up-down** axis.
+- **Roll:** rotation around the **front-back** axis.
+
+Each parameter can be any integer between **-180 and +180**. You define the 
+minimum and maximum value to search within - for example, pitch between -10 
+and +10 degrees.
+
+You can also preview what pitch, yaw, and roll look like using the manual 
+refine sliders underneath the Automatic Slice Detection button.
+
+### 3. Bayesian optimisation parameters
+
+- **Initial random points:** the number of random points to sample before 
+optimisation begins (default: 5).
+- **Bayesian iterations:** number of optimisation steps (default: 15).
+
+Bayesian optimisation works by first sampling a few random parameter 
+combinations, then using a probabilistic model (a Gaussian process) to 
+estimate which unexplored combinations are most promising. 
+
+At each step, it balances exploration (trying new regions) and exploitation 
+(refining near the current best result). This makes it much more efficient 
+than a brute-force grid search.
+
+### 4. Similarity metric
+
+You can choose the metric used to score similarity between the sample and 
+atlas slice.
+
+• **MI (Mutual Information)**
+
+Estimated via k-nearest neighbour entropy methods. MI measures statistical 
+dependence between two images – it is zero if they are independent, and 
+increases with stronger dependency.
+
+• **NCC (Normalised Cross-Correlation):**
+
+$$
+NCC(A,B) = \frac{\sum_i (A_i - \bar{A})(B_i - \bar{B})}
+{\sqrt{\sum_i (A_i - \bar{A})^2 \; \sum_i (B_i - \bar{B})^2}}
+$$
+
+Captures similarity in intensity patterns, invariant to linear rescaling 
+of intensities.
+
+• **SSIM (Structural Similarity Index):**
+
+$$
+SSIM(A,B) = 
+\frac{(2\mu_A \mu_B + C_1)(2\sigma_{AB} + C_2)}
+{(\mu_A^2 + \mu_B^2 + C_1)(\sigma_A^2 + \sigma_B^2 + C_2)}
+$$
+
+Captures perceptual differences in structure, luminance, and contrast.
+
+• **Combined:**
+
+Weighted combination of MI, NCC, and SSIM. You can customise the weight for 
+each metric.
+
+### 5. Start the optimisation
+
+Once parameters are confirmed, click **OK**. A progress bar will appear while 
+optimisation runs. When complete, the best-matching slice and rotation will 
+be displayed in the Napari viewer.
+
+You can continue to fine-tune results manually using the **pitch, yaw, and 
+roll sliders.**
+
+## Slab detection mode
+
+The Automatic Slice Detection widget supports both single-slice and slab 
+detection.
+
+The widget will **automatically detect** whether your moving image is a 
+single 2D slice or a 3D slab of multiple slices, and run the appropriate 
+optimisation procedure.
+
+How slab detection works:
+
+1.	The optimiser first matches the **first and last slices** of your slab to 
+the atlas using Bayesian optimisation.
+2.	It then interpolates the atlas Z-indices and rotation parameters (pitch, 
+yaw, roll) for all intermediate slices.
+3.	The slab is reconstructed into the atlas space, and your moving image is 
+automatically aligned as a 3D block.
+4.	As you scroll through Z in Napari, the pitch, yaw, and roll spinboxes 
+dynamically update to reflect the per-slice parameters.
+
+### Handling slab-to-atlas alignment:
+
+Depending on the relative depth of your slab compared to the atlas Z-range 
+between the matched endpoints, three cases are handled automatically:
+
+•	**Case 1 (Expansion):** If the atlas depth between the matched endpoints 
+is smaller than the slab, the target range is expanded outward until the 
+number of slices matches.
+
+•	**Case 2 (Exact Match):** If the atlas depth exactly equals the slab 
+depth, the slab is directly mapped slice-for-slice.
+
+•	**Case 3 (Subsampling):** If the atlas depth is larger than the slab, 
+slices are subsampled across the range to match the number of slab slices.
+
+## Logging and results
+
+All results, including the best slice and orientation, the final score, and 
+the optimisation parameters, are saved to a logging file. You can find this 
+in your system’s BrainGlobe directory:
+
+```
+<Path to your home directory>/.brainglobe/brainglobe_registration_logs/
+```
+
+This path is automatically created the first time you use BrainGlobe tools. 
+The logs can help you keep track of your registration parameters across 
+sessions.
+
+In addition to .txt summary logs, **detailed optimisation history** is also 
+stored. This includes:
+
+•	**Per-iteration images:** the rotated atlas slice evaluated at each 
+optimisation step is saved as an image. These are stored in subfolders named 
+_coarse_XXX_ (pitch/yaw/z search) and _fine_XXX_ (roll search).
+
+•	**Rotation matrices:** the 3×3 transformation matrix used for each 
+candidate slice is logged as a JSON-style object.
+
+•	**Metadata:** Each saved image and data object is annotated with 
+iteration parameters (pitch, yaw, roll, z-slice) and the similarity score.
+
+•	**Final summary:** the optimal pitch, yaw, roll, and z-slice are printed 
+to the log, along with scores before and after roll optimisation.
+
+These logs make it possible to retrace the entire optimisation process, 
+visually inspect why certain parameters were chosen, and reuse parameter 
+values for later experiments.
+
+## Recommended parameters and trade-offs
+
+•	**Z range:** Narrowing the range (e.g., 20 slices instead of the full 
+atlas) significantly reduces computation time while maintaining accuracy. 
+If unsure, start broad and refine later.
+
+•	**Rotation bounds:** If your sample is roughly aligned, set tighter pitch/
+yaw/roll bounds (±10–15°). Wider ranges (±90–180°) allow for more flexibility 
+but increase optimisation time.
+
+•	**Bayesian iterations:** More iterations improve accuracy but linearly 
+increase runtime. For typical use, 10–20 iterations provide a good balance 
+between speed and precision.
+
+•	**Similarity metric:** MI or the Combined metric often provide the most 
+robust alignment for noisy or partial data, though the best practice is to 
+test multiple metrics to see which performs best for your dataset.
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