CHANGELOG

# CHANGELOG

| Commit | Author | Date | Summary | Changes |
|--------|--------|------|---------|---------|

| b262bca | Anton Avramov | 2025-03-05 | Added GUI, fixed channel handling, fixed bugs, updated README, fixed docs. |
| e83b8f5 | Anton Avramov | 2025-02-06 | Bug fixes |
| a2ee43c | Anton Avramov | 2025-02-06 | Flatten image for cellpose model to segment the frame. Fixed .tif handling routines |
| 2862fb6 | Anton Avramov | 2025-02-06 | Corrected the cyanobacteria name to meet industry standards in run_segmentation.py |
| 2248a92 | Zach Maas | 2025-01-19 | Main repository documentation updates to reflect the segmentation script's output format. |
| 451d3bd | Anton Avramov | 2025-01-16 | Renamed the models to reflect names in the manuscript, added cypose-scratch-7002 model |
| de700db | Anton Avramov | 2025-01-16 | Reverted commits [c73b5ec, 2991927, 71cb502, fe49458, db44e03, bbe0937, 0460e63, 2691ca9] from 2025-01-16 due to file corruption. 
| 4f9f277 | Anton Avramov | 2025-01-15 | Cell counter script update |
| ba86f64 | Anton Avramov | 2024-10-10 | Uploaded better Anabaena 33047 segmentation model | Uploaded PCC 7002 classification model | Added script for cell counting |
| 4972ffc | Zach Maas | 2024-09-19 | Add benchmarking and training scripts for segmentation models | Added `benchmark_segmentation.sh`, `diff_masks.py`, `train_omnipose.sbatch` (131 insertions) |
| 63a171c | Zach Maas | 2024-09-19 | Add FILE_HASHES file for data integrity | Added `FILE_HASHES` (1 insertion) |
| 3d5d672 | Zach Maas | 2024-09-19 | Add size option and improve frame handling | Updated `CHANGELOG`, `README.md`, `run_segmentation.py`, `shell.nix`, `test_segmentation.sh` (102 insertions, 32 deletions) |
| d96b3bd | Zach Maas | 2024-09-19 | Add training script | Added `train_cellpose.sbatch` (24 lines) |
| 32f81a0 | Clair Huffine | 2024-09-14 | Updates on classifier processing | Updated 5 files, major additions to classification and segmentation scripts |
| ff14312 | Zach Maas | 2024-08-20 | Add trained models for collaborators | Added multiple trained models (22 files) for reference, force push required due to merge conflicts. Original date 2024-08-020, amended date 2024-09-09 |
| 562de9b | Zach Maas | 2024-03-27 | HTML Formatting Fix | Minor README update |
| 9122f90 | Zach Maas | 2024-03-27 | Small README update | Minor README change |
| 902f0a0 | Zach Maas | 2024-03-27 | Update segmentation script and README | Major updates to segmentation script, README, and configuration files |
| 4d7a6dc | Clair Huffine | 2024-02-21 | Classification updates | Added new classification models and updated scripts |
| 606c6df | Clair Huffine | 2024-02-06 | Added classification and segmentation analysis | Major additions to classification and segmentation comparison scripts |
| 957209a | Clair Huffine | 2024-01-29 | Added classifier output | Added new classification model and related scripts |
| e67dd4c | Zach Maas | 2024-01-26 | Push weekly updates and new model | Added new model and updated classification training script |
| 936f663 | Zach Maas | 2024-01-16 | Update segmentation script for multi-channel models | Enhanced segmentation and classification scripts |
| 0555c9a | Zach Maas | 2024-01-16 | Add preliminary anabaena models | Added new models and classification training script |
| 477532e | Zach Maas | 2023-11-28 | Formatting readme | Minor README update |
| 602bca6 | Zach Maas | 2023-11-28 | Update README for scientific accuracy | Minor README update |
| 3bee26d | Zach Maas | 2023-11-28 | Add LICENSE for scripts | Added LICENSE file |
| c7ebdaa | Zach Maas | 2023-11-28 | Update documentation and argument parsing | Updated README and segmentation script |
| 70b87ef | Zach Maas | 2023-11-28 | Add code and README for initial demonstration | Initial project setup with README, model, and scripts |