From 635f2db5f0157f266ab5ceedaa41048090b9af66 Mon Sep 17 00:00:00 2001
From: Sooyoung Cheong <64125280+c-sooyoung@users.noreply.github.com>
Date: Tue, 25 Aug 2026 15:03:00 +0900
Subject: [PATCH] added README and license

---
 LICENSE   | 19 +++++++++++++++++++
 readme.md | 26 ++++++++++++++++++++++++++
 2 files changed, 45 insertions(+)
 create mode 100644 LICENSE
 create mode 100644 readme.md

diff --git a/LICENSE b/LICENSE
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+++ b/LICENSE
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+Copyright (c) 2026 Sooyoung Cheong
+
+Permission is hereby granted, free of charge, to any person obtaining a
+copy of this software and associated documentation files (the "Software"),
+to deal in the Software without restriction, including without limitation the
+rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
+sell copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
diff --git a/readme.md b/readme.md
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+++ b/readme.md
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+# bo-ptycho
+
+This code is a (re)implementation of Bayesian Optimized ptychography in python for use at LEMON lab, used for
+
+- Optimization-based Thickness Estimation and FIB-induced Damage Characterization of TEM Sample via Multislice Electron Ptychography (manuscript)
+
+
+
+## Code usage
+
+Prerequisites:
+1. Create a python virtual environment with [requirements.txt](./requirements.txt)
+2. Download [fold_slice](#)
+2. Download [experimental data](#)
+
+Reconstruction and parameter optimization:
+1. Edit [config.yaml](./config.yaml)
+    - Example configurations can be found under `examples/silicon-fib/`
+    - Set io.input_data_path and io.result_dir as needed (WARNING: the result directory will be completely removed)
+    - Set ptycho.path to your fold_slice path
+2. Edit [job.sub](./job.sub)
+    - Set the SBATCH configurations as needed (especially `gres` and `output`)
+    - The number of GPUs should match bo.batch in config.yaml
+    - Set the virtual environment path
+    - Set the config.yaml path
+3. Submit the job via SLURM