Developers Meetings

[thompson318]

Notes and minutes from developers' meetings

[thompson318]

07/10/2021
Action: Targets for future research development
Action: Targets for future software development.

BARD: We want to allow BARD to be usable as an example of how to build a augmented reality application using SciKit-Surgery. This will involve a considerable amount of work in refactoring and writing tutorials etc. PySide and VTK seem to be rather buggy and lead to increasing problems with deployment and testing. Create issue SciKit-Surgery/scikit-surgerybard#77

[thompson318]

03/11/2021
Next work on the agenda.
Visualisations for surgeryVTK. Outline renderer for SmartSurgery
Atractsys
Longer Term: What could we do for a tutorial or workshop at MICCAI?

[mxochicale]

Thu 10 Nov 14:00:39 GMT 2022

Attendees: ST, MC, MX; chair: MC; Apologies: TD ; Absent:

1 Updates

MX:

• Last commit for /sksurgerynditracker/nditracker.py reached a coverage of 92.308% where the following points remain to be covered > Low code coverage scikit-surgerynditracker#31 (comment)
• Replication of tutorial01 under ubuntu22.04, fixing issues with py and vtk versions: Replicating tutorial (along with improvements) scikit-surgerytutorial01#31
• Add labels for priorities (p0-critial, p1-high, p2-medium, p3-low) in https://github.com/SciKit-Surgery/scikit-surgery/issues
• Quick review of the MICCAI Challenges (40 projects for 2022, number of pages are between 12 to 40 pages): http://www.miccai.org/special-interest-groups/challenges/miccai-registered-challenges/ more: http://www.miccai.org/special-interest-groups/challenges/
• summer school in July?, 2-page paper for https://www.hamlynsymposium.org/call-for-papers/, submission 31st January 2023 23:59 GMT?
• New projects with inertial sensors, hololens2, etc?

2 Pending

• none at the moment

3. General discussion and comments

NOTE. marks show the status of each point.

• Leave issues as they are but label them with priority (p0_critial, p1_high,p2_medium,p3_low)
• Steve will create an issue for vtk application
• Might be fusion of inertial sensors
• atracsys library https://www.atracsys-measurement.com/ to then move to fusion-data library
• Dependencies for https://github.com/UCL/scikit-surgeryopencvcpp and issues with OpenCV-headlines
• Branches older than 6 months should go
• Discussions around sustainability of software (perhaps see good practices that align well)
• Getting rid of surgeryopencvcpp.

4. Roadmap and actions

• MX Script a report for branches and get in touch with the leads!
• ST surgeryopencvcpp
• ST: vtk, py versioning
• open a new issue for pyside2 discussions (using pyside6), pyqt6, etc, in each indvitual projects initially,

If you feel I left something out, please add/edit it.

Thanks
Miguel

[mxochicale]

Thu 01 Nov 14:00:00 GMT 2022

Attendees: ST, MC, TD, MX; chair: MC; Apologies: ; Absent:

1 Updates

MX:

• Summary of branches in SciKit-Surgery repositories

  • 2 out of 36 activate branches https://github.com/SciKit-Surgery/scikit-surgeryvtk/branches
  • 1 out of 6 branches https://github.com/SciKit-Surgery/ndicapi/branches
  • 1 out of 4 activate branches https://github.com/SciKit-Surgery/scikit-surgerynditracker/branches
  • 1 out of 4 active branches https://github.com/SciKit-Surgery/scikit-surgerybard/branches
  • 1 out of 2 branches https://github.com/SciKit-Surgery/scikit-surgeryutils/branches
  • 0 out of 13 activate branches https://github.com/SciKit-Surgery/scikit-surgerycalibration/branches
  • 0 out of 12 activate branches https://github.com/SciKit-Surgery/scikit-surgeryimage/branches
  • 0 out of 10 activate branches https://github.com/SciKit-Surgery/scikit-surgeryopencvcpp/branches
  • 0 out of 6 activate branches https://github.com/SciKit-Surgery/scikit-surgeryfred/branches
  • 0 out of 5 activate branches https://github.com/SciKit-Surgery/scikit-surgerytorch/branches/all
  • 0 out of 5 activate branches https://github.com/SciKit-Surgery/browser_ar/branches
  • 0 out of 4 activate branches https://github.com/SciKit-Surgery/scikit-surgerytf/branches
  • 0 out of 4 activate branches https://github.com/SciKit-Surgery/scikit-surgerydocker/branches
  • 0 out of 3 branches https://github.com/SciKit-Surgery/cut-the-string/branches
  • 0 out of 3 activate branches https://github.com/SciKit-Surgery/luminance_study/branches
  • 0 out of 3 activate branches https://github.com/SciKit-Surgery/scikit-surgery/branches
  • 0 out of 3 activate branches https://github.com/SciKit-Surgery/scikit-surgeryarucotracker/branches
  • 0 out of 3 activate branches https://github.com/SciKit-Surgery/scikit-surgeryspeech/branches
  • 0 out of 3 activate branches https://github.com/SciKit-Surgery/snappysonic/branches
  • 0 out of 3 activate branches https://github.com/SciKit-Surgery/scikit-surgerycore/branches
  • 0 out of 2 activate branches https://github.com/SciKit-Surgery/scikit-surgeryglenoid-paper/branches
  • 0 out of 2 activate branches https://github.com/SciKit-Surgery/scikit-surgery-rse2021-poster/branches
  • 0 out of 2 activate branches https://github.com/SciKit-Surgery/scikit-surgeryfred-paper/branches
  • 0 out of 2 activate branches https://github.com/SciKit-Surgery/scikit-surgery-stats/branches
  • 0 out of 2 activate branches https://github.com/SciKit-Surgery/scikit-surgerychallenge/branches
  • repositories with one branch were not listed

• Issues

  • p1-high Remove dependendcy on scikit-surgeryopencvcpp scikit-surgerycalibration#46
  • p1-high: Can we implement outline rendering scikit-surgeryvtk#177
  • p2-medium pip dependencies can be included in a conda env PythonTemplate#59

• Others

  • Plans for Q4-2022, Q1-Q4-2023, Q1-2024

2 Pending

• none at the moment
• add MX as admin for https://github.com/SciKit-Surgery/PythonTemplate/labels

3. General discussion and comments

NOTE. marks show the status of each point.

• https://github.com/SciKit-Surgery/PythonTemplate/ might be used github actions (using different python versions) and locally tox!
• Discussions about plans and preparation on submitting Hardware interfaces at Hamlyn Symposium and future plans for RSE paper submission
• Look for previous papers/workshops https://www.hamlynsymposium.org/proceedings/

4. Roadmap and actions

• Discuss next steps for submission Hamlyn Symposium

If you feel I left something out, please add/edit it.

Thanks
Miguel

[mxochicale]

Thu 8 Dec 13:30:00 GMT 2022

Attendees: ST, MC, TD, MX; chair: MC; Apologies: ; Absent:

(1) Updates

MX:

• Updates

  • Pushed triangulation.py
  • Amend ci.yml to starting unit test with py3.7
  • Looking into other python implementations of triangulation.py (see few here)

• Issues

  • p1-high Remove dependendcy on scikit-surgeryopencvcpp scikit-surgerycalibration#46
  • p1-high: Can we implement outline rendering scikit-surgeryvtk#177
  • p2-medium pip dependencies can be included in a conda env PythonTemplate#59

• Others

  • Plans for Q4-2022, Q1-Q4-2023, Q1-2024

(2) Pending

• add MX as admin for https://github.com/SciKit-Surgery/PythonTemplate/labels

(3) General discussion and comments

• Discuss roadmap-for-sckit-surgery-2023-2024 (aims of the submission to Hamlyn Symposium, RSE conf)
• Discussions on the aims for submitting a workshop for Hamlyn Symposium
• pip wheel for mac for nditracker

(4) Roadmap, next steps and actions

• Implement unit test # Triangulate using OpenCV > https://github.com/SciKit-Surgery/scikit-surgerycalibration/blob/master/sksurgerycalibration/video/video_calibration_metrics.py#L174 then also do current migration!

If you feel I left something out, please add/edit it.

Thanks
Miguel

[mxochicale]

Thu 15 Dec 14:00:00- 14:30:00 GMT 2022

Attendees: ST, MC, MX; chair: MC; Apologies: TD ; Absent:

(1) Updates

MX:

• Updates

  • Added load_chessboard_arrays(): test_triangulate_points_with_hartley(): and test_triangulate_points_using_hartley_opencv(): https://github.com/SciKit-Surgery/scikit-surgerycalibration/blob/46-removing-scikit-surgeryopencvcpp/tests/algorithms/test_triangulate.py
  • Added and merged CI for py37, 38, 39, 310, 311 48 clean unit test scikit-surgerycalibration#49
  • Merged pylintfix 50 pylintfix scikit-surgerycalibration#51

• Issues

  • p1-high Remove dependendcy on scikit-surgeryopencvcpp scikit-surgerycalibration#46
  • p1-high: Can we implement outline rendering scikit-surgeryvtk#177
  • p2-medium pip dependencies can be included in a conda env PythonTemplate#59

• Plans for Q4-2022, Q1-Q4-2023, Q1-2024

  • Hamlyn Symposium Workshop (deadline 16th January 2023),
    • organisers mention that there is no proceedings for workshops.
    • emailed them to ask further questions about available budget for speaker's travel and accommodation cost, and references on how you foresee a well organised and relevant workshop
    • Contacted Evs to ask about students' projects using aurora tracker
  • Call for Talks, Workshops, or Walkthroughs (deadline March 2023) at the RSE conference (Early Sep 2023)
    • ask to RSE slack about examples of previous submissions.
  • ?

(2) Pending

• ...

(3) General discussion and comments

• Discussion on the migration of the unit test for matrix operations. Matt recommends numpy.matmul for simpler operation than more complicated ones cv2.gemm. MX to hopefully finish this next 20-dec.
• Steve share progress of surface models for VTK, using outline_actor functions, discussing around the use of constructor parameters but requires to use a mapper along with opacity and colour. Other way is using config file.
• Duplication of models: surface_model_loader.py (file parsing) don't need a config file, vtk_surface_model_directory_loader.py but they are different according to Matt. Straigh forward path is to add an option with user cases. If going to the route of refactoring, get it rid of one and perhaps bid.

(4) Roadmap, next steps and actions

• Finalise Remove dependendcy on scikit-surgeryopencvcpp scikit-surgerycalibration#46
• Last meeting of the project on 21-Jan-2022.

If you feel I left something out, please add/edit it.

Thanks
Miguel

[mxochicale]

Thu 12 Jan 14:00:00 GMT 2023

Attendees: ST, MC, MX; chair: MC; Apologies: TD ; Absent:

(1) Updates

MX:

• Updates
  • Successful Removal scikit-surgeryopencvcpp dependencies from surgerycalibration. Merged in the master 46 - Removing scikit-surgeryopencvcpp dependencies  scikit-surgerycalibration#47
  • ..
• Current issues
  • p1-high pyside6 scikit-surgeryvtk#187
  • p3-low cv2.triangulatePoints method generates different decimal values of the reconstructed points. scikit-surgerycalibration#53
  • ...
• Plans for Q4-2022
  • Preparation of Hamlyn Symposium Workshop (deadline 16th January 2023),
  • Touch base with Evs' students to understand status and next steps
  • Preparing in2research project
  • ...

(2) Pending

• ...

(3) General discussion and comments

• Hamlyn Symposium Workshop preparation
• Compatibility vtk and pyside6 , could we muck vtk Widget only. Qt, Qt vtk and derived class. Boxing to work withing a week.

(4) Road map, next steps and actions

• Finalise pyside6 scikit-surgeryvtk#187
• [ ]

If you feel I left something out, please add/edit it.

Thanks
Miguel

[mxochicale]

Thu 19 Jan 14:00:00 GMT 2023

Attendees: ST, MC, MX; chair: MC; Apologies: TD ; Absent:

(1) Updates

MX:

• Updates

  • Submitted proposal for Hamlyn Symposium Workshop (deadline 16th January 2023),
  • Identified issues with QVTKRenderWindowInteractor scikit-surgeryvtk v1.1.0
  • Supporting Evs' students with sensor synchronisation
  • Suggested to add released notes on versions of scikit-surgeryvtk and others Release notes scikit-surgeryvtk#197
  • Found that scikit-surgeryutils depends on PySide2>=5.12.0 which will be the next aim for the library.
  • ...

• Current issues

  • p1-high pyside6 scikit-surgeryvtk#187
  • p2-medium ModuleNotFoundError: No module named 'vtkmodules'  scikit-surgerytutorial01#34
  • p3-low cv2.triangulatePoints method generates different decimal values of the reconstructed points. scikit-surgerycalibration#53
  • ...

• Plans for Q1-2023

  • Preparation of Hamlyn Symposium Paper [extended deadline 12 noon (GMT) 25th January 2023) ]
  • Preparing in2research project with a 250 words summary (deadline 27 Jan 2023)
  • ...

(2) Pending

• ...

(3) General discussion and comments

• Getting the right combination of dependencies and versions
• VTK 8 to VTK 9: Steve adds a flag self.Initialize(), self.Start()
• working with the minimum version then those changes will be propagated in others
• ...

(4) Road map, next steps and actions

• Compatibility of QVTKRenderWindowInteractor pyside6 scikit-surgeryvtk#187
• ...

If you feel I left something out, please add/edit it.

Thanks
Miguel

[mxochicale]

Thu 2 Feb 15:00:27 GMT 2023

Attendees: ST, MC, MX; chair: MC; Apologies: TD ; Absent:

Updates

• MX
  • pyside6 scikit-surgeryvtk#187
  • Debugging unit tests in a systematic-like manner  scikit-surgeryvtk#203
  • ...
• Plans for Q1-2023
  • Hamlyn Symposium Workshop/Paper
  • in2research project

General discussion and comments

• Discussions of failing remote test Debugging unit tests in a systematic-like manner  scikit-surgeryvtk#203
• Failures in remote pylint: Run pylint --rcfile=tests/pylintrc  scikit-surgeryvtk#204
• Help and Support #115 (comment)
• ...

Road map, next steps and actions

• MX sorted out issues related to export QT_DEBUG_PLUGINS=1 : https://github.com/SciKit-Surgery/scikit-surgeryvtk/actions/runs/4075975998/jobs/7023086558
• MX carry on with Debugging unit tests in a systematic-like manner  scikit-surgeryvtk#203
• MX/TD check tutorials https://mphy0026.readthedocs.io/en/latest/summerschool/bard.html

Pending

• ...
• ...

If you feel I left something out, please add/edit it.

Thanks
Miguel

[mxochicale]

Thu 9 Feb 14:13:15 GMT 2023

Attendees: ST, MX, TD; chair: ; Apologies: MC ; Absent:_

Updates

• MX
  • Debugging unit tests in a systematic-like manner  scikit-surgeryvtk#203
  • Fatal Python error: Segmentation faults  scikit-surgeryvtk#202
  • pyside6 scikit-surgeryvtk#187
  • ...
• Plans for Q1-2023
  • in2research project
  • Hamlyn Symposium Workshop/Paper

General discussion and comments

• versions of https://github.com/SciKit-Surgery/scikit-surgerybard to run home-based tutorials https://mphy0026.readthedocs.io/en/latest/summerschool/bard.html
• issues with pyside2 and pyside6

Road map, next steps and actions

• Carry on with pyside6 scikit-surgeryvtk#187
• MX Updates to Launch 2023 UCL/MPHY0026#64

Pending

• MX/TD check tutorials https://mphy0026.readthedocs.io/en/latest/summerschool/bard.html
• ...

If you feel I left something out, please add/edit it.

Thanks
Miguel

[mxochicale]

Thu 16 Feb 14:00:15 GMT 2023

Attendees: ST, MX, TD; chair: ; Apologies: MC ; Absent:_

Updates

• MX
  • Pre-releases 2.0a1, 2.0.b1, 2.0.rc1 and final release 2.0.0 scikit-surgeryvtk#205
  • Debugging unit tests in a systematic-like manner  scikit-surgeryvtk#203
  • Fatal Python error: Segmentation faults  scikit-surgeryvtk#202
  • pyside6 scikit-surgeryvtk#187
• TD
  • conflicting requirements were solved Updates to Launch 2023 UCL/MPHY0026#64
• General
  • in2research project was submitted
  • Waiting for notification of Hamlyn Symposium Workshop submission

General discussion and comments

• Conflicts on VTK pipeline and mask size in VTKRenderingGenerator and discussed potential solutions
• Testing tag before doing the pypi release.
• Update of tutorials
• Steve will be in conference next week

Road map, next steps and actions

• MX Carry on with Pre-releases 2.0a1, 2.0.b1, 2.0.rc1 and final release 2.0.0 scikit-surgeryvtk#205
• MX to update tutorial https://github.com/SciKit-Surgery/scikit-surgeryvtk/blob/master/docs/tutorials/overlay_window.ipynb

Pending

If you feel I left something out, please add/edit it.

Thanks
Miguel

[mxochicale]

Thu 23 Feb 13:30:51 GMT 2023

Attendees: ST, MX, TD, ST; chair:MC ; Apologies: ; Absent:_

Updates

• MX
  • Solved conflicts on VTK pipeline and mask size in VTKRenderingGenerator
  • Pre-releases 2.0a1, 2.0.b1, 2.0.rc1 and final release 2.0.0 scikit-surgeryvtk#205
  • Debugging unit tests in a systematic-like manner  scikit-surgeryvtk#203
  • Fatal Python error: Segmentation faults  scikit-surgeryvtk#202
  • pyside6 scikit-surgeryvtk#187
• General
  • in2research project was submitted
  • Waiting for notification of Hamlyn Symposium Workshop submission
  • 2 pages abstract for the rami-icra-2023-workshop [deadline 15th March 2023]:

General discussion and comments

• Solving issues with vtk pipeline and window containers with QtWidgets.QWidget
• Skipping linux test for test_interlaced_stereo_window.py
• BARD tutorials: opencv-headless pickup pyside2 > Are we still pulling in opencv non headless? scikit-surgerybard#109

Road map, next steps and actions

• MX tidied code and skip tests that includeVTKStereoInterlacedWindow and others that are failing under linux. Open issues to report of the status of the skipped tests.
• MX: Carry on with Pre-releases 2.0a1, 2.0.b1, 2.0.rc1 and final release 2.0.0 scikit-surgeryvtk#205
• MX: Address issues with VTKStereoInterlacedWindow and pytest -v -s tests/widgets/test_interlaced_stereo_window.py::test_stereo_overlay_window
• MX share draft for rami-icra-2023

Pending

• Testing tag before doing the pypi release.
• MX to update tutorial https://github.com/SciKit-Surgery/scikit-surgeryvtk/blob/master/docs/tutorials/overlay_window.ipynb
• next steps after migration of pyside2 to pyside6 with vtk will be looking vtk dependence in surgery-utils and passing tests

If you feel I left something out, please add or edit it.

Thanks
Miguel

[mxochicale]

Thu 2 Mar 14:00:00 GMT 2023

Attendees: ST, MX, TD, ST; chair:MC ; Apologies: ; Absent:_

Updates

• MX
  • Raised PR 187 - pyside6 scikit-surgeryvtk#208
  • Prepare Pre-releases 2.0a1, 2.0.b1, 2.0.rc1 and final release 2.0.0 scikit-surgeryvtk#205
  • New issue Class hierarchy is a bit messy for few visualization pipelines scikit-surgeryvtk#207
  • New issue Release v2.0.0 PythonTemplate#65
• General
  • in2research list will be shared in mid-March
  • Waiting for notification of Hamlyn Symposium Workshop submission
  • Preparing 2 pages abstract for the rami-icra-2023-workshop [deadline 15th March 2023]:

General discussion and comments

• AR application in skitsurgery-parallax and on vtk widgets,
• Prioritise vtk development
• Main README for projects, plan to tidied up (minimal maintenance ), outdated website https://github.com/SciKit-Surgery/scikit-surgery/tree/web
• How to install conda env with requirements > https://scikit-surgerytutorial02.readthedocs.io/en/latest/01_Starting_Out.html
  • document conda
  • remove tox which is not used in github action
• Repositories should have version and os point out to github actions
• Python version 3.7 end-of-life, 2023-06-27
• Check coverage, list of skipped tests in ci and add them as comments

Road map, next steps and actions

• ..
• Add labels p0 Critical priority to prioritise issues and starts solving them https://github.com/SciKit-Surgery/scikit-surgeryutils/issues
• Testing tag before doing the pypi release.
• Migrating pyside2 to pyside6 scikit-surgeryutils#53

Pending

• MX to update tutorial https://github.com/SciKit-Surgery/scikit-surgeryvtk/blob/master/docs/tutorials/overlay_window.ipynb
• ...

If you feel I left something out, please add or edit it.

Thanks
Miguel

[mxochicale]

Thu 9 Mar 14:00:15 GMT 2023

Attendees: ST, MX, TD, ST; chair:MC ; Apologies: ; Absent:_

Updates

• MX
  • release candidate 2.0.rc0 for scikit-surgeryvtk Pre-releases 2.0a1, 2.0.b1, 2.0.rc1 and final release 2.0.0 scikit-surgeryvtk#205
  • Added priority labels to scikit-surgeryutils issues https://github.com/SciKit-Surgery/scikit-surgeryutils/issues
  • Migrating pyside2 to pyside6 scikit-surgeryutils#53
• General
  • Hamlyn Symposium Workshop submission (HSME23) has been accepted
  • in2research list will be shared in mid-March
  • Preparing 2 pages abstract for the rami-icra-2023-workshop [deadline 15th March 2023]:

General discussion and comments

• Discussion around list of speakers HSME23
• Updates on release candidate 2.0.rc0 and local and remote unit tests of scikit-surgeryutils

Road map, next steps and actions

• Finalise list of local tentative seekers for HSME23, and sharing on 10 March 2023
• Use decorators to skip OS specific unit test and carry on with Migrating pyside2 to pyside6 scikit-surgeryutils#53

Pending

• MX to update tutorial https://github.com/SciKit-Surgery/scikit-surgeryvtk/blob/master/docs/tutorials/overlay_window.ipynb
• ...

If you feel I left something out, please add or edit it.

Thanks
Miguel

[mxochicale]

Thu 16 Mar 14:00:00 GMT 2023

Attendees: ST, MX, TD, ST; chair:MC ; Apologies: ; Absent:_

Updates

• MX
  • added decorators to skip specific local and remote unit tests
  • updated pylint version and refactor scripts for cleaner linting Migrating pyside2 to pyside6 scikit-surgeryutils#53
  • solved local unit tests for pytest -v -s tests/test_sksurgerytextoverlay.py (related to vtk and pyside6 workflows)
• General
  • Updated list of speakers, added timeline, template to invite speakers and drafts to advertise Hamlyn Symposium Workshop submission (HSME23)
  • Preparing 2 pages abstract for the rami-icra-2023-workshop [Extended deadline 24th March 2023]:
  • in2research list will be shared in mid-March (waiting for updates)

General discussion and comments

• Discussing about HSME23 next steps to contacting speakers.
• Expense requests for paper submissions

Road map, next steps and actions

• MX: carry on with unit test for scikit-surgeryutils, contacting speakers and sharing rami-icra-2023 2-pages paper.

Pending

• MX to update tutorial https://github.com/SciKit-Surgery/scikit-surgeryvtk/blob/master/docs/tutorials/overlay_window.ipynb
• ...

If you feel I left something out, please add or edit it.

Thanks
Miguel

[mxochicale]

Thu 4 May 14:00:00 BST 2023

Attendees: ST, MX, TD; chair: ; Apologies:MC ; Absent:_

Updates

• MX
  • Finalising list of speakers Hamlyn Symposium Workshop submission (HSME23).
  • Final release 2.0.0 for scikit-surgeryvtk > Final release 2.0.0  scikit-surgeryvtk#216
• ST
  • snappysonic pyside6 Update to PySide6 snappysonic#26

General discussion and comments

• Meeting Idil to plan kick-off of the "OSSS Call: sustainability dashboards", starting next Tuesday 9 of May 2023 with in-person meetings on Thursdays.

Road map, next steps and actions

• MX Final release 2.0.0 for scikit-surgeryvtk and raises issues for scikit-surgeryutils; scikit-surgerybard; scikit-surgerytutorial02

Pending

• MX. In May I will prepare prototype for in2research project. Timeline: 8 weeks and need to take place between 1 June and 31 Aug 2023. This will lead to further discussions on a project that aligns with COMPASS, WEISS and career plan of MX.
• MX to update tutorial https://github.com/SciKit-Surgery/scikit-surgeryvtk/blob/master/docs/tutorials/overlay_window.ipynb

If you feel I left something out, please add or edit it.

Thanks
Miguel

[mxochicale]

Thu 11 May 14:00:00 BST 2023

Attendees: ST, MX, TD; chair: ; Apologies:MC ; Absent:_

Updates

• MX
  • Program for "Open-Source Software for Surgical Technologies" at Hamlyn Symposium Workshop submission (HSME23) is online https://www.hamlynsymposium.org/events/open-source-software-for-surgical-technologies/
  • Final release 2.0.0 for scikit-surgeryvtk > Final release 2.0.0  scikit-surgeryvtk#216
    • solved X Error of failed request: BadWindow (adding export QT_DEBUG_PLUGINS=0 and export QT_QPA_PLATFORM=xcb to ci.yml)
    • updates of vtk>=9.2.6 and PySide6>=6.5.0
    • add .readthedocs.yaml and build docs
    • solving Update tutorials scikit-surgeryvtk#206
• ST
  • kick-off of sustainability dashboards: https://github.com/SciKit-Surgery/scikit-surgery-stats/discussions/11

General discussion and comments

• Discussed tutorials Rendering Generator and VTKOverlayWindow , leave Distance Field Calcualtion & Voxelisation

Road map, next steps and actions

• MX PR for Final release 2.0.0 for scikit-surgeryvtk

Pending

• MX. In May I will prepare prototype for in2research project. Timeline: 8 weeks and need to take place between 1 June and 31 Aug 2023. This will lead to further discussions on a project that aligns with COMPASS, WEISS and career plan of MX.
• MX to update tutorial https://github.com/SciKit-Surgery/scikit-surgeryvtk/blob/master/docs/tutorials/overlay_window.ipynb
• Final releases for scikit-surgeryutils; scikit-surgerybard; scikit-surgerytutorial02

If you feel I left something out, please add or edit it.

Thanks
Miguel

[mxochicale]

Thu 18 May 14:00:00 BST 2023

Attendees: ST, MX; chair:MC ; Apologies:TD ; Absent:

Updates

• MX
  • Preparing advertisement of "Open-Source Software for Surgical Technologies" at Hamlyn Symposium Workshop submission (HSME23) https://www.hamlynsymposium.org/events/open-source-software-for-surgical-technologies/
  • Final release 2.0.0 for scikit-surgeryvtk > Final release 2.0.0  scikit-surgeryvtk#216
    • solved building in readthedocs https://readthedocs.org/projects/scikit-surgeryvtk/builds/20737747/
    • resolved build errors (e.g indentation, duplication, missing quotes, blank lines, etc)
    • updates tox.ini with requirements-docs and other packages (removed nbsphinx)
  • in2research project
    • working prototype to collect and analyse image and motion sensor data
    • preparation of scripts and documentation
  • joining Surg3 call, prepare one minute introduction and one slide (submission 24 of May)
• ST
  • sustainability dashboards
    • Integration of cron scheduler to dashboard
    • Idil is presenting dashboard at ARC Collaborations Group Meeting on 23 of May 2023

General discussion and comments

• Posters for ARC showcase (todo: target audience? ), interactive poster that we can use demos AR, ST fw poster to MX
• sphinx-build -M html . build warnings can be addressed in next release and focus in final releases in coming days.
• QTimer with GUI can be a good threading mechanism (see https://stackoverflow.com/questions/42279360/does-a-qtimer-object-run-in-a-separate-thread-what-is-its-mechanism but might be other good docs)

Road map, next steps and actions

Owner	Next steps and actions
MX	PR for Final release 2.0.0 for scikit-surgeryvtk

Pending

• MX:
  • update tutorial https://github.com/SciKit-Surgery/scikit-surgeryvtk/blob/master/docs/tutorials/overlay_window.ipynb
  • Final releases for scikit-surgeryutils; scikit-surgerybard; scikit-surgerytutorial02

If you feel I left something out, please add or edit it.

Thanks
Miguel

[mxochicale]

Thu 25 May 14:00:12 BST 2023

Attendees: ST; chair: MX; Apologies:MC, ST ; Absent:

Updates

• MX
  • Starting advertisement of "Open-Source Software for Surgical Technologies" at Hamlyn Symposium Workshop submission (HSME23) https://www.hamlynsymposium.org/events/open-source-software-for-surgical-technologies/
  • Final release 2.0.0 has been published in pypi https://pypi.org/project/scikit-surgeryvtk/2.0.0/
  • in2research project
    • starting date of the placement is 12th of June, and working prototype is ready for the placement holder
  • Surg3 call
    • submitted one minute introduction and one slide
• ST/MX
  • sustainability dashboards
    • Integration of cron scheduler to dashboard
    • preparation of Workshop for the The South London RSE (Abstract submission deadline Tuesday 30th May 2023 ) https://rslondon.ac.uk/rslondonsoutheast2023/cfs/

General discussion and comments

Road map, next steps and actions

Owner	Next steps and actions
MX	Prepare PRs for Final releases of scikit-surgeryutils; scikit-surgerybard; scikit-surgerytutorial02

Pending

• MX:
  • update tutorial https://github.com/SciKit-Surgery/scikit-surgeryvtk/blob/master/docs/tutorials/overlay_window.ipynb

If you feel I left something out, please add or edit it.

Thanks
Miguel

[mxochicale]

Thu 1 June 14:00:00 BST 2023

Attendees: ; chair: MX; Apologies:MC, ST, ST ; Absent:

Updates

• MX
  • Release notes of final release 2.0.0
  • Raised issue for final release 2.0.0 of utils Final release 2.0.0  scikit-surgeryutils#57
  • in2research project
    • training session for the placement. We will start on 12th of June (prototype is already working)
  • Advertisement of HSME23 workshop
• ST/MX
  • sustainability dashboards
    • Integration of cron scheduler to dashboard
    • Submitted abstract on sustainable dashboards for the The South London RSE https://rslondon.ac.uk/rslondonsoutheast2023/cfs/

General discussion and comments

• look for doc, docs,

Road map, next steps and actions

Owner	Next steps and actions
MX	Prepare PRs for Final releases of scikit-surgerybard; scikit-surgerytutorial02

Pending

• MX:
  • update tutorial https://github.com/SciKit-Surgery/scikit-surgeryvtk/blob/master/docs/tutorials/overlay_window.ipynb

If you feel I left something out, please add or edit it.

Thanks
Miguel

[mxochicale]

Thu 15 Jun 14:00:00 BST 2023

Attendees: ; chair: MX; Apologies:MC, ST, ST ; Absent:

Updates

• MX
  • Addressing final release 2.0.0 of utils Final release 2.0.0  scikit-surgeryutils#57
  • Addressing version of opencv-contrib-python-headless AttributeError: module 'cv2.aruco' has no attribute 'Dictionary_get' scikit-surgeryutils#58; PR 58 - opencv contrib python headless scikit-surgeryutils#59
  • in2research project "AI-based evaluation of surgical skills".
    • Kick-off meeting with Sujon 12th of June, doing literature review and doing https://github.com/SciKit-Surgery/scikit-surgerytutorial02
  • Advertisement of HSME23 workshop
• ST/MX
  • sustainability dashboards
    • Submitted abstract on sustainable dashboards for the The South London RSE https://rslondon.ac.uk/rslondonsoutheast2023/cfs/

General discussion and comments

• utils depends on surgerycalibration, so the workflow will be to fix unit test in scikit-surgerycalibration
• versions of opencv-contrib-python-headless using the same version unless it is require to update new versions
• comments to improve scikit-surgerytutorial02/issues/36

Road map, next steps and actions

Owner	Next steps and actions
MX	Prepare PRs for Final releases of scikit-surgeryutils
MX	Create scikit-surgeryvtk 2.0.1 with opencv-contrib-python-headless>=4.2.0.32

Pending

• MX:
  • final releases of scikit-surgerybard; scikit-surgerytutorial02
  • update tutorial https://github.com/SciKit-Surgery/scikit-surgeryvtk/blob/master/docs/tutorials/overlay_window.ipynb

If you feel I left something out, please add or edit it.

Thanks
Miguel

[mxochicale]

Thu 22 Jun 14:08:17 BST 2023

Attendees: ; chair: MX; Apologies:MC, ST, ST ; Absent:

Updates

• MX
  • Updates for final releases 2.0.0 for scikit-surgeryutils , bard and v1.0.0 tutorial02
• ST/MX
  • sustainability dashboards
    • template is ready and replicated 30 cookieninja with scikit surgery template base scikit-surgery-stats#31

General discussion and comments

• discussing the source of ERROR: Could not install packages due to an OSError: [Errno 2] No such file or directory: >Feedback and comments from the replication of the tutorial02 by Sujon Hekim scikit-surgerytutorial02#36 (comment)

Road map, next steps and actions

Owner	Next steps and actions
MX	Prepare PRs for Final releases of bard tutorial02
MX,ID,ST	Review SciKit-Surgery/scikit-surgery-stats#31

Pending

• MX:
  • final releases of scikit-surgerybard; scikit-surgerytutorial02
  • update tutorial https://github.com/SciKit-Surgery/scikit-surgeryvtk/blob/master/docs/tutorials/overlay_window.ipynb

If you feel I left something out, please add or edit it.

Thanks
Miguel

[mxochicale]

Thu 29 Jun 14:00-14:30 BST 2023

Attendees: ST, TD; chair: MX; Apologies:MC; Absent:

Updates

• MX
  • Updates on successful Hamlin workshop, following release of the talks and white paper
  • Tutorial02 has been replicated by Sujon, leading to coming changes in final release 1.0.0
• ST/MX
  • sustainability dashboards
    • remove pipeline for pypi package is running at 30 cookieninja with scikit surgery template base scikit-surgery-stats#31
    • preparation of presentation for The South London RSE Workshop, Monday 17th July 2023 at Imperial College London

General discussion and comments

• Hamlyn workshop: preparation on the white-paper, audio-recording was missing for steve (so asked to send audio), update speakers about video recording, slide release and contact speakers for travel reimbursement
• Finding study cases for NVIDIA Clara AGX with WEISS researchers.

Road map, next steps and actions

Owner	Next steps and actions
MX	Prepare PRs for Final releases of tutorial02
MX,ID,ST	Review SciKit-Surgery/scikit-surgery-stats#31

Pending

• MX:
  • update tutorial https://github.com/SciKit-Surgery/scikit-surgeryvtk/blob/master/docs/tutorials/overlay_window.ipynb

If you feel I left something out, please add or edit it.

Thanks
Miguel

[mxochicale]

Thu 6 Jul 14:03:31 BST 2023

Attendees: ST, MC; chair: MX; Apologies:TD; Absent:

Updates

• MX

  • PR for Tutorial02 is ready to be merged 39 - final release 1.0.0 scikit-surgerytutorial02#40
  • in2research week4: Sujon has completed tutorial02 and we have started to install dependencies for inertial sensor and video streaming. Steve showed us training kit that can be used for skill surgical assessment experiments.

• ST/MX

  • sustainability dashboards
    • Idil has made grade progress with https://github.com/SciKit-Surgery/scikit-surgery-stats/tree/30-cookieninja-with-scikit-surgery-template-base (adding details on how to use it)

General discussion and comments

• NVIDIA Clara AGX plans on cloud vs on-device deployment and training, which hardware device will be supported, overlaying text or image to frames, do we need a new library, graphical user interfaces or both?
• Matt has successfully prototyped bard-based application using our latest final releases https://github.com/SciKit-Surgery/scikit-surgeryvtk/releases/tag/v2.0.1
• Adopting conda for scikit-surgery libs and potentially remove tox for improve user experience (e.g. Env creation from python 3.7 not working M1 Apple Silicon Mac (Miniconda 3) conda/conda#12206). This require further discussion but perhaps a good starting point would be from the template Release v2.0.0 PythonTemplate#65

Road map, next steps and actions

Owner	Next steps and actions	Accountable (approver)	Support	Consulted	Informed
MX	SciKit-Surgery/PythonTemplate#65	-	-	-	-
MX	Explore capabilities of nvidia-clara-agx	-	-	-	-
MX,ID,ST	Review SciKit-Surgery/scikit-surgery-stats#31	-	-	-	-

Pending

• MX:
  • update tutorial https://github.com/SciKit-Surgery/scikit-surgeryvtk/blob/master/docs/tutorials/overlay_window.ipynb
• MC
  • Atracsys tracker interface, new repo?, search API

If you feel I left something out, please add or edit it.

Thanks
Miguel

[mxochicale]

Thursday 13 Jul 14:00:00 BST 2023

Attendees: ST; chair: MX; Apologies:TD, MC; Absent:

Updates

• MX

  • Updating python template following good software practices and aiming to a seamless usability experience for its users.
  • in2research week5: I have installed ubuntu 22.04 on Alienware-m17 due to other issues on windows that slowed down our progress (setting up of permissions for notebooks and building dll drivers for sensor). Similarly, we have started demo-data prototype with one inertial sensor and one usb-endoscope camera.
  • Preparing release of video recordings "Open-Source Software for Surgical Technologies" and expenses request of my claimants
  • Created discussing topics to follow up atracsys development and one relevant issue What are your short/long term plans for your repo? luoshaqi/atracsysTracker#1
  • I can connect to nvidia-clara-agx, next steps is to check the hardware capabilities and share document of the plans.

• ST/MX

  • sustainability dashboards
    • Idil is preparing presentation with our support. We are presenting on Monday 17th "Towards substantiable dashboards for open-source software projects" > https://rslondon.ac.uk/rslondonsoutheast2023/abstracts/#ft6

General discussion and comments

• Integration of inheritance diagrams with sphinx and readthedocsin Python templates to have better understanding of pipeline mechanism in the libraries (i.e., Class hierarchy is a bit messy for few visualization pipelines scikit-surgeryvtk#207)
• Make use of the tutorial02 as a test base for the updates in python template

Roadmap, next steps and actions

Owner	Next steps and actions	Accountable (approver)	Support	Consulted	Informed
MX	SciKit-Surgery/PythonTemplate#65	ST	-	-	-
MX	Explore capabilities of nvidia-clara-agx	ST,MC	-	-	-
MX,ID,ST	Review SciKit-Surgery/scikit-surgery-stats#31	MX,ST	-	-	-

Pending

• MX:
  • update tutorial https://github.com/SciKit-Surgery/scikit-surgeryvtk/blob/master/docs/tutorials/overlay_window.ipynb

If you feel I left something out, please add or edit it.

Thanks
Miguel

[mxochicale]

Thu 2 Nov 11:23:35 GMT 2023

Attendees: ST; chair: MX; Apologies:TD, MC; Absent:

I am updating our meeting minutes once a week for better consistency and keep everyone in the loop.

Updates

• MX
  • Received UCL Open Science Award for the Category "Professional Services Staff Activities" https://github.com/oss-for-surgtech/ucl-open-science-awards-2023
  • Submitted Hackathon project and currently tidying up activities https://github.com/SciKit-Surgery/cmicHACKS2
  • Presented "Towards lightweight transformer-based models with multimodal data for low-latency surgical applications" at the Fast Machine Learning for Science last 26th Sep Presentation for Fast Machine Learning for Science [Tue 26/09/2023; 17:00 - 17:15] mxochicale/sentient#32
  • ...
• ST
  • new version of https://github.com/SciKit-Surgery/ndicapi for https://github.com/SciKit-Surgery/scikit-surgerynditracker
  • ...

General discussion and comments

• Tidying up activities for Hackathon project for training and optimising models

Roadmap, next steps and actions

Owner	Next steps and actions	Accountable (approver)	Support	Consulted	Informed
MX	Preparations for activities https://github.com/SciKit-Surgery/cmicHACKS2	ST,MC	-	-	-
MX	Software/hardware architectures using nvidia-clara-agx (mid/end Nov)	ST,MC	-	-	-
...	...	...	...	...	...

Pending

• MX:
  • Python template Release v2.0.0: Release v2.0.0 PythonTemplate#65 (added requests for venv by Joao and check of pypy password authentication by ST )
  • To discuss venue of white paper: Selecting venue of publication of the paper oss-for-surgtech/white-paper#3
  • update tutorial https://github.com/SciKit-Surgery/scikit-surgeryvtk/blob/master/docs/tutorials/overlay_window.ipynb

If you feel I left something out, please add, edit it or let me know..

Thanks
Miguel

[mxochicale]

Tue 7 Nov 14:26:59 GMT 2023

Attendees: ST; chair: MX; Apologies:TD, MC; Absent:

Updates

• MX
  • Preparation for Hackathon project and currently tidying up activities https://github.com/SciKit-Surgery/cmicHACKS2 and slides https://scikit-surgery.github.io/cmicHACKS2/slides/slides.html#/
  • ...
  • ...
• ST
  • ...
  • ...

General discussion and comments

• Tidying up activities for Hackathon project for training and optimising models
• Venue of white paper: Selecting venue of publication of the paper oss-for-surgtech/white-paper#3 which International Journal of Computer Assisted Radiology and Surgery seems to be an appropriate one via IPCAI submission
• atracsys -- fusionTrack 500: Meeting with Bernhardt, Sylvain on Wed 08/11/2023 10:00 - 11:00 to discuss
  • the possibility of providing a script for our SDK and
  • your CI solve the issue of converting the NDI geometry files to our format

Roadmap, next steps and actions

Owner	Next steps and actions	Accountable (approver)	Support	Consulted	Informed
MX	Preparations for activities https://github.com/SciKit-Surgery/cmicHACKS2	ST,MC	-	-	-
MX	Software/hardware architectures using nvidia-clara-agx (mid/end Nov)	ST,MC	-	-	-
...	...	...	...	...	...

Pending

• MX:
  • Python template Release v2.0.0: Release v2.0.0 PythonTemplate#65 (added requests for venv by Joao and check of pypy password authentication by ST )
  • update tutorial https://github.com/SciKit-Surgery/scikit-surgeryvtk/blob/master/docs/tutorials/overlay_window.ipynb

If you feel I left something out, please add, edit it or let me know..

Thanks
Miguel

[thompson318]

Thu 14/16 Nov 2023

Attendees: ST MC ; chair: MX; Apologies: ; Absent:

Updates

• MX
  • CMIC hackathon 2023: We won best team name "real-[good]-time" from the 9 group projects. Further details of our achievements are here https://scikit-surgery.github.io/cmicHACKS2/work-achieved/#/title-slide
  • Debugging results of segmentation predictions https://github.com/SciKit-Surgery/nvdia-clara-agx/tree/33-colonoscopy_segmentation/examples/colonoscopy_segmentation#screenshots-of-colonoscopy_segmentationpy
  • ...
• ST
  • This follows up on work that my MSc student (Innes) did on using shadows as a depth cue. If we combined the above depth estimation operator with tool tracking (https://github.com/nvidia-holoscan/holohub/tree/main/applications/endoscopy_tool_tracking) and a VTK illumination model we'd have everything thing we need for virtual shadowing. Just link together the software, get running on the Clara AGX and we have a demo running in real time on the Clara. Write a grant 24 months post doc + 24 months RSE, sorted.
  • ...

General discussion and comments

• nvidia-clara-agx
  • uses cases (tool tracking, sensor fusion, segmentation, etc)
  • arquitecture
• The Hamlyn Symposium on Medical Robotics
  • Venue of white paper: Selecting venue of publication of the paper oss-for-surgtech/white-paper#3 which International Journal of Computer Assisted Radiology and Surgery seems to be an appropriate one via IPCAI submission. "Journal of Software: Evolution and Process" might be other option
• atracsys -- fusionTrack 500; Bernhardt, Sylvain
  • Aiming to have working and document setup
  • how to make a a seamless experience for any user using our SciKit-Surgery (using just binaries of atracsysSDK)?
  • Maybe we don't have bandwidth for the following points but I just listing them here
    • Make use of SKSBaseTracker to initialise the tracker in the constructor, loading geom files and then grab data every time it is polled.
    • your CI solve the issue of converting the NDI geometry files to our format

Roadmap, next steps and actions

Owner	Next steps and actions	Accountable (approver)	Support	Consulted	Informed
MX	focusing on solving colonoscopy_segmentation on clara-agx	ST,MC	-	-	-
MX	...	ST,MC	-	-	-
...	...	...	...	...	...

Pending

• MX:
  • Python template Release v2.0.0: Release v2.0.0 PythonTemplate#65 (added requests for venv by Joao and check of pypy password authentication by ST )
  • update tutorial https://github.com/SciKit-Surgery/scikit-surgeryvtk/blob/master/docs/tutorials/overlay_window.ipynb

If you feel I left something out, please add, edit it or let me know..

Thanks
Miguel

[mxochicale]

21/23 Nov 2023

Attendees: ST MC ; chair: MX; Apologies: ; Absent:

Updates

• MX
  • Merged branch 33-colonoscopy_segmentation to main and link relevant sections to run colonoscopy_segmentation > examples/colonoscopy_segmentation
  • Working on conversion NCHW to NHWC for colonoscopy_segmentation using graph_surgeon.py
  • Team alignment to work on end-to-end python-based app for PitSurg model
• ST
  • ...
  • ...

General discussion and comments

• nvidia-clara-agx
  • ...
• The Hamlyn Symposium on Medical Robotics
  • Venues of white paper: Selecting venue of publication of the paper oss-for-surgtech/white-paper#3 which International Journal of Computer Assisted Radiology and Surgery and "Journal of Software: Evolution and Process". Next steps, draft structure questionnaire of 10 aspects for OSS4Surg
  • ...
• atracsys -- fusionTrack 500; Bernhardt, Sylvain
  • Aiming to have working and document setup with a seamless experience for any user using our SciKit-Surgery (using just binaries of atracsysSDK). Maybe block two weeks once we have examples from Sylvain
  • ...

Roadmap, next steps and actions

Owner	Next steps and actions	Accountable (approver)	Support	Consulted	Informed
MX	focusing on standalone app with scaffolding to run PitSurg model	ST,MC	-	-	-
MX	...	ST,MC	-	-	-
...	...	...	...	...	...

Pending

• MX:
  • Set a low-priority: Python template Release v2.0.0: Release v2.0.0 PythonTemplate#65 (added requests for venv by Joao and check of pypy password authentication by ST )
  • Set a low-priority: update tutorial https://github.com/SciKit-Surgery/scikit-surgeryvtk/blob/master/docs/tutorials/overlay_window.ipynb
  • ...

If you feel I left something out, please add, edit it or let me know..

Thanks
Miguel

[mxochicale]

28/30 Nov 2023

Attendees: ST MC ; chair: MX; Apologies: ; Absent:

Updates

• MX
  • PitSurgApp (1.0.0-alpha)
    • Added model preparation details (simplification, rebinding and transference to cagx).
    • Added data preparation details using one image frame (using ffmeg with convert_video_to_gxf_entities.py).
    • Added endoscopic_pituitary_surg.py
    • using bring_your_own_model. Relevant to start using operators, workflows and config files.
    • Included details for terminal logs and python application window output
  • V4L2VideoCapture0, holoscan.core.Tracker https://docs.nvidia.com/holoscan/sdk-user-guide/flow_tracking.html
  • VideoStreamRecorderOp
• ST
  • ...
  • ...

General discussion and comments

• nvidia-clara-agx
  • https://github.com/nvidia-holoscan/holohub/tree/main/applications/multiai_endoscopy/app_dev_process#phase-4-porting-the-multi-ai-application-to-c
• The Hamlyn Symposium on Medical Robotics
  • Organise next workshop (submission deadline 19th Jan 2023)
  • Venues of white paper: Selecting venue of publication of the paper oss-for-surgtech/white-paper#3 which International Journal of Computer Assisted Radiology and Surgery and "Journal of Software: Evolution and Process". Next steps, draft structure questionnaire of 10 aspects for OSS4Surg
  • ...
• atracsys -- fusionTrack 500; Bernhardt, Sylvain
  • Aiming to have working and document setup with a seamless experience for any user using our SciKit-Surgery (using just binaries of atracsysSDK). Maybe block two weeks once we have examples from Sylvain
  • python templates?

Roadmap, next steps and actions

Owner	Next steps and actions	Accountable (approver)	Support	Consulted	Informed
MX	integrating V4L2VideoCapture0 in PitSurgApp	ST,MC	-	-	-
MX	...	ST,MC	-	-	-
...	...	...	...	...	...

Pending

• MX:
  • Set a low-priority: Python template Release v2.0.0: Release v2.0.0 PythonTemplate#65 (added requests for venv by Joao and check of pypy password authentication by ST )
  • Set a low-priority: update tutorial https://github.com/SciKit-Surgery/scikit-surgeryvtk/blob/master/docs/tutorials/overlay_window.ipynb
  • ...

If you feel I left something out, please add, edit it or let me know..

Thanks
Miguel