Recon recommendations

.gitmodules

@@ -0,0 +1,16 @@
+[submodule "src/mapping_robot"]
+	path = src/mapping_robot
+	url = https://github.com/imr-framework/mapping_robot/
+	branch = dev_ws_2026
+[submodule "src/passive_shimming"]
+	path = src/passive_shimming
+	url = https://github.com/imr-framework/passive_shimming
+	branch = dev_ws_2026
+[submodule "src/pyCoilGen"]
+	path = src/pyCoilGen
+	url = https://github.com/sairamgeethanath/pyCoilGen
+	branch = dev_ws_2026
+[submodule "src/console"]
+	path = src/console
+	url = https://github.com/sairamgeethanath/console
+	branch = dev_ws_2026

README.md

@@ -27,3 +27,56 @@ openmrd validate my_scanner/scanner.yaml
 
 ## Status
 This is a **v0.1** proposal meant to bootstrap community discussion. PRs welcome!
+
+<div align="center">
+  <img src="https://github.com/user-attachments/assets/d8a7c6e1-9337-4a7d-88c9-b72ed52cbec9" width="200">
+</div>
+
+ **Building: Repositories list - please use the dev_ws_2026 branch for all submodules** 
+1.  Magnet: design and simulation
+2.  Magnet: construction
+3.  [Field mapping robot](https://github.com/imr-framework/mapping_robot/)
+4.  [Passive shimming including 3D STL file generation](https://github.com/imr-framework/passive_shimming)
+5.  [Amplifiers: Gradient, RF TX and RF RX - 3rd party - Larry Wald/Martinos/MGH](https://tabletop.martinos.org/index.php?title=Main_Page)
+6.  [Planar gradient coil design using pycoilgen](https://github.com/sairamgeethanath/pyCoilGen) or [previous effort](https://github.com/imr-framework/planar_gradient_coil_design/tree/main)
+7.  RF coil: design and simulation
+8.  RF coil: construction
+9.  [Spectrometer - 3rd party - FLOCRA; part of console software download](https://github.com/vnegnev)
+10. [Pulse sequence design using Pypulseq](https://github.com/imr-framework/pypulseq)
+11. [Console software](https://github.com/sairamgeethanath/console)
+12. Phantom 
+13. Scanner log and outputs
+
+
+ **Playing: Repositories list** 
+ 1. [Virtual Scanner Tabletop Games](https://github.com/imr-framework/vs-tabletop/tree/delta-diy)
+ 2. [Virtual Scanner](https://github.com/imr-framework/virtual-scanner/)
+
+## Our image currently looks like ....
+<img src="https://github.com/user-attachments/assets/423c93c2-c405-448e-8fd6-d84fc44a69a9" width="200">
+
+
+
+
+
+## Potential student projects
+
+***Hardware**
+1.  Field mapping robot - Design covers, wiring and a user interface
+2.  Passive shims - explore new geometries and new optimization methods
+3.  RF coils - Bat head coil matching the anatomy of its head
+
+***MR physics***
+1. Pulse sequences - Robust RF frequency finder, refine calibration sequences - RF power, gradient  
+2. Image reconstruction - Multiple k-space filters 
+
+***Software***
+1. Console - automate install and startup 
+2. Interface virtual scanner games with the console using the Pulseq format
+
+***New experiments***
+1. T1 mapping
+2. T2 mapping
+
+**Acknowledgement**:
+1. Johns Hopkins Provost DELTA award, 2024 

contributing.md

@@ -0,0 +1,246 @@
+# Contributing to Delta DIY MRI
+
+Welcome! 👋  
+Thank you for contributing to the Delta DIY MRI ecosystem.
+
+This project spans multiple repositories and disciplines (hardware: magnet, gradients, RF;  firmware and software:spectrometer, acquisition, reconstruction; mechanical designs of parts and phantoms, etc.), and this guide is designed to help **participants and mentors collaborate effectively** during the workshop and beyond.
+
+👉 Start here: [Step-by-Step Workshop Contribution Guide](#step-by-step-workshop-contribution-guide)
+---
+
+## Table of Contents
+
+- Getting Started
+- Ways to Contribute
+- Branching Strategy
+- Development Workflow
+- Pull Request Guidelines
+- Code Review Process
+- Workshop-Specific Guidelines
+- After the Workshop
+- Multi-Repository Coordination
+- Commit Message Guidelines
+- Code Style & Best Practices
+- Getting Help
+
+---
+
+## Getting Started
+
+1. Fork the repository (if external contributor)
+
+2. Clone your fork
+   git clone <your-fork-url>
+   cd <repo-name>
+
+3. Add upstream
+   git remote add upstream <original-repo-url>
+
+4. Sync with upstream
+   git fetch upstream
+   git checkout dev
+   git merge upstream/dev
+
+---
+
+## Ways to Contribute
+
+- Hardware design (coils, magnet, electronics)
+- RF systems and tuning
+- Gradient design and optimization
+- Reconstruction algorithms
+- Software tools and GUIs
+- Documentation and tutorials
+- Testing and validation
+
+---
+
+## Branching Strategy
+
+| Branch Type | Purpose | Stability |
+|------------|--------|----------|
+| main       | Production-ready code | High |
+| dev        | Active development | Medium |
+| feature/*  | New features | Low |
+| workshop/* | Rapid experiments | Very Low |
+| hotfix/*   | Urgent fixes | High |
+
+Core rules:
+- No direct commits to main
+- All changes via Pull Requests
+- Branch from dev (unless hotfix)
+- Keep PRs small and focused
+
+Naming conventions:
+
+Feature branches:
+feature/<module>-<description>
+
+Workshop branches:
+workshop/day1-rf
+workshop/team-recon
+
+Hotfix branches:
+hotfix/<issue-description>
+
+---
+
+## Development Workflow
+
+1. git checkout dev
+   git pull origin dev
+
+2. git checkout -b feature/<name>
+
+3. git add .
+   git commit -m "feat: short description"
+
+4. git push origin feature/<name>
+
+5. Open Pull Request to dev
+
+---
+
+## Pull Request Guidelines
+
+Each PR should include:
+- Description of the change
+- Problem being solved
+- How it was tested
+- Screenshots / plots if applicable
+
+Checklist:
+[ ] Code runs without errors
+[ ] No broken dependencies
+[ ] Documentation updated
+
+---
+
+## Code Review Process
+
+- At least one mentor approval required - please refer to https://delta-diy-mri.github.io/ for the appropriate mentor
+- Focus on correctness, clarity, reproducibility
+- Discussion encouraged - please use GitHub discussions - https://github.com/delta-diy-mri/delta-diy-mri.github.io/discussions
+
+---
+
+## Workshop-Specific Guidelines
+
+- Prioritize learning and speed of trying out implementations
+- Use workshop branches for experiments
+- Merge into dev daily
+- Coordinate within teams
+
+---
+
+## After the Workshop
+
+- Reduce workshop branches
+- Enforce stricter reviews
+- Add CI/testing
+- Stabilize main
+
+---
+
+## Multi-Repository Coordination
+
+- Use consistent branch names
+- Reference related PRs:
+
+Depends on: repo-name#123  
+Related to: repo-name#456
+
+---
+
+## Commit Message Guidelines
+
+Format:
+<type>: <short description>
+
+Types:
+- feat
+- fix
+- docs
+- refactor
+- test
+
+---
+
+## Code Style & Best Practices
+
+- Keep code modular and readable
+- Comment non-obvious logic
+- Prefer clarity over cleverness
+- Avoid breaking existing functionality
+
+---
+
+## Getting Help
+
+- Open a draft PR early
+- Ask a mentor
+- Use GitHub Issues
+- Discuss with your team
+
+---
+
+## Final Notes
+
+This project enables hands-on MRI system building and interdisciplinary collaboration.
+
+When in doubt: open a PR early and ask for feedback.
+
+Happy building! 🧲
+
+
+
+## Overview
+This repo uses submodules. Contributions may involve:
+- Main repo
+- Submodules
+
+## Workflow Summary
+1. Fork repo
+2. Clone with submodules
+3. Create branch
+4. Edit main or submodule
+5. Commit, push
+6. Open PR
+
+---
+
+# Step-by-Step Workshop Contribution Guide
+
+## 1. Fork
+Click Fork on GitHub - https://github.com/imr-framework/open-mri/
+
+## 2. Clone
+```bash
+git clone --recurse-submodules <your-fork-url>
+cd <repo-name>
+git checkout dev_ws_2026
+```
+
+## 3. Branch
+git checkout -b my-feature
+
+## 4A. Edit Main Repo
+git add .
+git commit -m "change"
+
+## 4B. Edit Submodule
+cd submodule
+git checkout -b change
+git commit -m "update"
+git push
+
+## Update pointer
+cd ..
+git add submodule
+git commit -m "update pointer"
+
+## 5. Push
+git push
+
+## 6. PR
+Open PR on GitHub

default_package/scanner.yaml → diy_mri_2026_package/scanner.yaml

@@ -85,7 +85,7 @@ subsystems:
   rf:
     tx:
       type: solenoid
-      f0_hz: 14900000.0
+      f0_hz: 11500000.0
       q_factor: 100.0
       impedance_ohm: 50.0
       pmax_w: null
@@ -94,7 +94,7 @@ subsystems:
       files: {}
     rx:
       type: solenoid
-      f0_hz: 14900000.0
+      f0_hz: 11500000.0
       q_factor: 150.0
       impedance_ohm: 50.0
       pmax_w: null

src/openmrd/demo_openmri.py

@@ -3,7 +3,7 @@
 sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..")))
 sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), "..")))
 
-from src.openmrd.models import ScannerManifest, GradAxis, Gradients, RFChannel, RF, Magnet, Spectrometer, Console, Subsystems, Metadata
+from src.openmrd.models import *
 
 TEMPLATES = {
     "halbach_lowfield": {

src/openmrd/demo_openmri_Ctype.py

@@ -18,7 +18,7 @@
 import argparse, os, sys, json, yaml
 sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..")))
 sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), "..")))
-from src.openmrd.models import ReconstructionManifest, ScannerManifest, GradAxis, Gradients, RFChannel, RF, Magnet, Spectrometer, Console, Subsystems, Metadata
+from src.openmrd.models import *
 
 TEMPLATES = {
     "c_type_permanent": {
@@ -30,10 +30,22 @@
                 "y":{"gmax_mTm":25,"slew_Tm_s":35,"resistance_ohm":2.5,"inductance_mH":5.2},
                 "z":{"gmax_mTm":20,"slew_Tm_s":30,"resistance_ohm":3.0,"inductance_mH":6.1}
             }},
-            "rf": {"tx":{"type":"solenoid","f0_hz":14.9e6,"q_factor":100,"impedance_ohm":50},
-                   "rx":{"type":"solenoid","f0_hz":14.9e6,"q_factor":150,"impedance_ohm":50}},
+            "rf": {"tx":{"type":"solenoid","f0_hz":11.5e6,"q_factor":100,"impedance_ohm":50},
+                   "rx":{"type":"solenoid","f0_hz":11.5e6,"q_factor":150,"impedance_ohm":50},
+                   "shielding":"copper"},
+            "recon_pipeline": {
+                "openmrd_version": "0.1",
+                "metadata": {"name":"C-Type-OpenMRD","organization":"DIY MRI","license":"MIT","contributors":["Researcher1", "Engineer1"],"created":"2025-08-27","description":"C-type permanent magnet design with N52 discs"},
+                "reconstruction_parameters": {"algorithm":"GRAPPA","acceleration_factor":2}
+            },
             "spectrometer":{"model":"RedPitaya-122","sampling_rate_hz":122e6,"bit_depth":16,"max_tx_freq_hz":50e6},
-            "console":{"name":"mri4all","os":"Linux","api":"Python gRPC","pulseq_support":True,"latency_ms":3.0}
+            "console":{"name":"mri4all","os":"Linux","api":"Python gRPC","pulseq_support":True,"latency_ms":3.0},
+            "recon": {"name": "open-lf-recon","framework": "Python","backend": "PyTorch","device": "cuda","latency_ms": 12.5,
+                "batch_size": 2,"input_format": "kspace","output_format": "image","complex_data": true,"use_kspace_recon": true,
+                "use_classical_denoising": true,"use_motion_correction": false,"use_super_resolution": true,"use_dl_reconstruction": true,
+
+                "model_name": "3D-UNet-SRR","model_checkpoint": "models/srr_unet.pth","physics_informed": true,"coil_sensitivity_maps": true,"field_strength": 0.05
+            }
         }
     }
 }
@@ -123,7 +135,7 @@ def main():
     """
     # Initialize with default arguments
     class Args:
-        package = "default_package"
+        package = "diy_mri_2026_package"
         template = "c_type_permanent"
         manifest = os.path.join(package, "scanner.yaml")
         func = None