Repository navigation

Port virtual_staining examples into applications/cytoland - #409

Merged

edyoshikun merged 47 commits into

modular-viscy-stagingfrom

cytoland-virtual-staining-examples

May 18, 2026

Merged

Port virtual_staining examples into applications/cytoland#409
edyoshikun merged 47 commits into
modular-viscy-stagingfrom
cytoland-virtual-staining-examples

Commits on Apr 24, 2026
- Exempt examples/ from docstring and line-length lint rules
  edyoshikun
  committed
  c07f9c9
- Port VS_model_inference demos from main into applications/cytoland
  edyoshikun
  committed
  89a0b82
- Port dlmbl_exercise tutorial from main into applications/cytoland
  edyoshikun
  committed
  0a9aab3
- Extend examples/ lint exemption to cover E402 and F821
  edyoshikun
  committed
  7bf9a4b
- Port vcp_tutorials from main into applications/cytoland
  edyoshikun
  committed
  08f5979
- Document ported examples in cytoland README
  edyoshikun
  committed
  2dbbac5
- Port phase_contrast tutorial from main into applications/cytoland
  edyoshikun
  committed
  c8542e1
- Teach PyTorch Lightning in the dlmbl exercise
  edyoshikun
  committed
  e3b27aa
- Sharpen dlmbl exercise teaching material
  edyoshikun
  committed
  c5cfe6a
- Apply 2025 DL@MBL feedback to dlmbl exercise
  edyoshikun
  committed
  6b156d3
- Migrate dlmbl setup from conda to uv
  edyoshikun
  committed
  63d96a1
- Replace SSIM with microSSIM in dlmbl exercise
  edyoshikun
  committed
  8bd4ea9
Commits on May 1, 2026
- Point dlmbl exercise to zarrv3 datasets
  edyoshikun
  committed
  34af4f1
- Rename dlmbl_exercise to dl-course-exercise
  edyoshikun
  committed
  4453627
- Split dl-course-exercise setup into TA and student scripts
  edyoshikun
  committed
  f5ce816
- Bump dl-course-exercise to Python 3.13 and viscy>=0.5.0a0
  edyoshikun
  committed
  2eae363
- Polish dl-course-exercise solution.py
  edyoshikun
  committed
  15b6f16
- Polish prose in dl-course-exercise solution.py
  edyoshikun
  committed
  7dbdaa6
- Port Task 2.5 (fluorescence -> phase) from DL@Janelia exercise
  edyoshikun
  committed
  ae01b60
Commits on May 18, 2026
- Potential fix for pull request finding
  
  edyoshikun
  and
  Copilot
  authored
  1f92f92
- Potential fix for pull request finding
  
  edyoshikun
  and
  Copilot
  authored
  5fc1d7c
- Potential fix for pull request finding
  
  edyoshikun
  and
  Copilot
  authored
  52b969e
- Potential fix for pull request finding
  
  edyoshikun
  and
  Copilot
  authored
  bc71142
- Potential fix for pull request finding
  
  edyoshikun
  and
  Copilot
  authored
  26be25e
- Potential fix for pull request finding
  
  edyoshikun
  and
  Copilot
  authored
  7bbe987
- Potential fix for pull request finding
  
  edyoshikun
  and
  Copilot
  authored
  dc5a855
- Potential fix for pull request finding
  
  edyoshikun
  and
  Copilot
  authored
  3f772ec
- Potential fix for pull request finding
  
  edyoshikun
  and
  Copilot
  authored
  c5d0eb9
- Potential fix for pull request finding
  
  edyoshikun
  and
  Copilot
  authored
  22d9549
- Potential fix for pull request finding
  
  edyoshikun
  and
  Copilot
  authored
  7df7457
- Potential fix for pull request finding
  
  edyoshikun
  and
  Copilot
  authored
  891cd4e
- Potential fix for pull request finding
  
  edyoshikun
  and
  Copilot
  authored
  1ffb236
- Potential fix for pull request finding
  
  edyoshikun
  and
  Copilot
  authored
  acae30b
- Potential fix for pull request finding
  
  edyoshikun
  and
  Copilot
  authored
  a738d94
- Potential fix for pull request finding
  
  edyoshikun
  and
  Copilot
  authored
  1ca6fa1
- Potential fix for pull request finding
  
  edyoshikun
  and
  Copilot
  authored
  968c720
- Potential fix for pull request finding
  
  edyoshikun
  and
  Copilot
  authored
  5dd202f
- Potential fix for pull request finding
  
  edyoshikun
  and
  Copilot
  authored
  83dfa24
- Potential fix for pull request finding
  
  edyoshikun
  and
  Copilot
  authored
  0a0933d
- Apply suggestions from code review
  
  edyoshikun
  and
  Copilot
  authored
  f1794d7
- Apply suggestions from code review
  
  edyoshikun
  and
  Copilot
  authored
  3a12a95
- demos: remove invalid `architecture` kwarg from HCSDataModule calls
  
  edyoshikun
  and
  claude
  committed
  830170a
- demo_vscyto_w_ttas: apply precomputed FOV stats normalization
  
  edyoshikun
  and
  claude
  committed
  84662fe
- phase_contrast setup: resolve cytoland path from script location
  
  edyoshikun
  and
  claude
  committed
  7c10bdf
- phase_contrast solution: drop unused trainer, make GPU placement explicit
  
  edyoshikun
  and
  claude
  committed
  119c301
- dl-course solution: fix DATA_ROOT semantics, TTA ordering, GPU loads
  
  edyoshikun
  and
  claude
  committed
  8e089b0
- dl-course README: recommend solution.ipynb path first, warn about task cells
  
  edyoshikun
  and
  claude
  committed
  0698483

Commits

Commits on Apr 24, 2026

Commits on May 1, 2026

Commits on May 18, 2026