# 1:1 Blessing + Shannon
- ICCV was a scam
- CVPR paper (deadline: Nov 11)
- Mitochondria review paper
---
# Friday, Sept 9, 11am
ICCV paper submitted
Cilia review paper submitted (or ready)
Neurocomputing paper in-progress
- SSCL paper
CVPR
- undetermined topic related to cilia
Mito review paper in-progress
- PLoS Computational Biology
1:1 Blessing + Shannon
===
- **Date:** August 12th, 2022, 10:00am
- **Agenda**
1. Follow up from August 8
- [ ] Continued with experiments on data augmentation with GAN and SSCL methods for cilia project
- [ ] Completed work on the literature review section on AAAI paper
- [ ] Submitted my abstract to AAAI conference on Monday, August 8
2. Goals for the week of August 15
- [ ] Complete my experiments on data augmentation with GAN and SSCL methods for AAAI paper and post codes on GitHub
- [ ] Validate my experiments on Moco, SimCLR, SimSiam,SwAV and BYOL with cilia datasets and ground truth
- [ ] Format cilia review paper and submit to IEEE Access Journal
- [ ] Complete the AAAI paper and submit to Neurocomputing since I couldn't submit full paper by August 15 deadline and my appeal to AAAI conference organizers for one week extension was declined.
- **Date:** August 5th, 2022, 10:00am
- **Agenda**
1. Follow up from July 29
- [ ] Continued with experiments on data augmentation with GAN and SSCL methods for cilia project
- [ ] Completed work on the literature section on AAAI paper
- [ ] Worked on my abstract for submission to AAAI conference on Monday, August 8
2. Goals for the week of August 8
- [ ] Complete my experiments on data augmentation with GAN and SSCL methods for AAAI paper and post codes on GitHub
- [ ] Validate my experiments on Moco, SimCLR, SimSiam,SwAV and BYOL with cilia datasets and ground truth
- [ ] Complete my abstract and submit to AAAI conference on Monday, August 8
- [ ] Suspended all work on cilia and Mitochondria review papers until after submitting AAAI paper on August 15
- **Date:** July 29, 2022, 10:00am
- **Agenda**
1. Follow up from July 22
- [ ] Continued with experiments on data augmentation with GAN and SSCL methods for cilia project
- [ ] Completed work two tables of 1) software tools and 2) deep learning for cilia review papers
- [ ] Completed work on the first subsection in the literature section on AAAI paper
2. Goals for the week of August 1st
- [ ] Complete my experiments on data augmentation with GAN and SSCL methods for AAAI paper and post codes on GitHub
- [ ] Complete the cilia review paper by Formatting the tables of 1) software tools and 2) deep learning
- [ ] Complete the write-up on the rest of literature section on AAAI paper (Deadline is August 15)
- [ ] Start to put finishing touches to Mitochondria review paper
:::info
- **Date:** July 22, 2022, 10:00am
- **Agenda**
1. Follow up from July 15
- [ ] Posted codes for ICCV 2022 paper on GitHub
- [ ] Submitted ICCV paper on 19 July
- [ ] Started experiments on data augmentation with GAN and SSCL methods for cilia project
- [ ] Started work on two tables of 1) software tools and 2) deep learning for cilia and Mito segmentation review papers
- [ ] Started work on the first 2 subsections on literature section on AAAI paper
2. Goals for the week of July 25
- [ ] Continue with my experiments on data augmentation with GAN and SSCL methods for AAAI paper on 20 July
- [ ] Complete the tables of 1) software tools and 2) deep learning for cilia and Mito segmentation review papers
- [ ] Complete the write-up on the first 2 subsections on literature section on AAAI paper (Deadline is August 15)
:::info
- **Date:** July 15, 2022, 10:00am
- **Agenda**
1. Follow up from July 1
- [ ] Posted codes for ICCV 2022 paper on GitHub in the week of 11 July
- [ ] Created masks on Ornet dataset for ICCV 2022 paper evaluation
- [ ] Wrote study justification paragraph for ICCV paper
- [ ] Downloaded cilia masks dataset
- [ ] Started experiments on data augmentation with GAN and SSCL methods for cilia project
- [ ] Struggled with ICCV paper template
2. Goals for next week
- [ ] Complete evaluation section on ICCV paper and submit on 19 July
- [ ] Continue with my experiments on data augmentation with GAN and SSCL methods for AAAI paper on 20 July
- [ ] Write the first 2 subsections on literature section on AAAI paper
- [ ] Create tables of imaging modalities on cilia and mitochondrial review papers
- **Participants:**
- Blessing
- Shannon
- **Host:** Shannon
:::
:arrows_counterclockwise: Follow-up from July 1
---
All the following points are from numerous previous meetings documented here in the hackmd. None of this is new. It all reflects where the PIP came from.
- [ ] [Review the Feb 28 meeting notes](https://hackmd.io/vaxcrC_STXm3uE5Op49okQ#-Responsibilities) for core QRG postdoc responsibilities
- [ ] Regular updates on progress. This takes many forms:
- GitHub issues: creating new ones, closing old ones, updating open ones
- **Created new personal repos within the past week**
- **Created new QRG repos within the past 24 hours**
- **A handful of new issues**
- **No closed or updated issues**
- Pushing code to GitHub (ideally linking it to open issues)
- **No code pushes since last meeting**
- Updating the weekly hackmd notes with your progress
- **No hackmd updates in weeks**
- Engagement in Slack
- **Asking for collaborators for new cilia project**
- Weekly 1:1s
1. Set clear and unambiguous goals
- **Goals seem clear from 1:1s, but change unexpectedly or are not met**
2. Lay out **in detail** how those goals will be achieved and what key steps need to be hit along the way
- **No details have been spelled out, aside from PIP, which only rehashed much of what was already in hackmd.**
3. Provide **regular updates** on your progress (GitHub, hackmd, Slack, zoom)
- **Updates have so far only come in the form of 1:1s and Slack, which tend to involve new and unannounced directions or no notable progress.**
**What blockers to these goals exist?**
**Outline all possible details toward achieving these goals.**
**Provide a timeline toward achieving these goals.**
:red_circle: Milestones
---
- Fully automated methods for the detection and segmentation of Mitochondria in microscopy images
- This is the ICCV paper I'm working on to submit on 19 July
- Improving the intelligibility of ciliopathy diagnostic model via self-supervised contrastive learning methods
- This is the AAAI conference paper I'm working on to submit on 15 August
- Literature review on deep learning frameworks for cilia image segmentation
- This is the cilia review paper I'm working on to submit on 31 July
- A review and discussion of deep learning frameworks for the detection, segmentation, and analysis of Mitochondrial morphology from microscopic cell images
- This is the mitochondrial review paper I'm working on to submit on 31 July
- ### **But where is the CODE that will demonstrate these?**
:dart: Goals for next week
---
- [ ] Labels for cilia and mitochondria data
- [ ] GAN for data augmentation (?)
- [ ] Provide actionable framework to the Contrastive Coding Cilia paper
- [ ] **Provide detailed breakdown of project timeline: major milestones, actionable tasks, predicted blockers, and proposed workarounds.**
- [ ] Install and use Putty https://www.putty.org/
## Notes
<!-- Other important details discussed during the meeting can be entered here. -->
Cilia data
- did the correction last night (what does that mean??)
GitHub personal account
- moved things over to QRG GitHub
Cilia videos
- are there special features to look out for?
- https://docs.google.com/document/d/16EfZKMi0jdJq_YiQNFyGT8tV5hHmt_Mz5SF9jWBDHeU/edit#
Found napari difficult to use
- using Label Studio and Fiji Image Annotator
Dropped VS Code in favor of Spyder and JupyterLab
- easier to view images and videos
---
:::info
- **Date:** July 1, 2022, 10:00am
- **Agenda**
1. Follow up from June 24
2. Milestones review
3. Goals for next week
- **Participants:**
- Blessing
- Shannon
- **Host:** Shannon
:::
:arrows_counterclockwise: Follow-up from June 24
---
Were any of these done? If so, check them off as you complete them.
**NO CHECKLIST ADDED LAST WEEK.**
- [Review the Feb 28 meeting notes](https://hackmd.io/vaxcrC_STXm3uE5Op49okQ#-Responsibilities) for core QRG postdoc responsibilities
- **Regular updates** on progress. This takes many forms:
- GitHub issues: creating new ones, closing old ones, updating open ones
- Pushing code to GitHub (ideally linking it to open issues)
- **Updating the weekly hackmd notes with your progress** (that's why we're doing this!)
- Engagement in Slack
- Weekly 1:1s
1. Set clear and unambiguous goals
2. Lay out **in detail** how those goals will be achieved and what key steps need to be hit along the way
3. Provide **regular updates** on your progress (GitHub, hackmd, Slack, zoom)
**No code pushes to GitHub. No GitHub issues updated. No discussions started or participated in on Slack. No goals, no details, NO UPDATES in the past week.**
:red_circle: Milestones
---
**What are our current goals?**
- [ICCV 2022](https://waset.org/computer-vision-conference-in-september-2022-in-vancouver) paper (SciPy topic, with some modified methods (???))
- Contrastive coding cilia segmentation ([ICML 2023](https://icml.cc/Conferences/FutureMeetings), January 2023 deadline; [MICCAI 2023](http://www.miccai.org/events/upcoming-conferences/), Feb-Mar 2023 deadline)
**What blockers to these goals exist?**
**Outline all possible details toward achieving these goals.**
**Provide a timeline toward achieving these goals.**
:dart: Goals for next week
---
- [ ] Continue working on the submitted ICCV 2022 paper for possible submission to the journal, Neurocomputing https://www.journals.elsevier.com/neurocomputing
- [ ] Provide actionable framework to the Contrastive Coding Cilia paper
- [ ] Ground truth labels for cilia + ornet datasets
## Notes
<!-- Other important details discussed during the meeting can be entered here. -->
- Current ICCV paper lacks justification of the methods
- Also lacks any comparison with existing methods
- Submit to Neurocomputing
- Somewhat niche, but if work is tailored correctly, it could fit.
> Neurocomputing welcomes theoretical contributions aimed at winning further understanding of neural networks and learning systems, including, but not restricted to, architectures, learning methods, analysis of network dynamics, theories of learning, self-organization, biological neural network modelling, sensorimotor transformations and interdisciplinary topics with artificial intelligence, artificial life, cognitive science, computational learning theory, fuzzy logic, genetic algorithms, information theory, machine learning, neurobiology and pattern recognition.
- analysis of network dynamics
- machine learning and pattern recognition
- AAAI is a good conference
- Want to do some work without training data (?)
- Unsupervised learning?
---
:::info
- **Date:** June 24, 2022, 10:00am
- **Agenda**
1. Follow up from May 17
2. Milestones review
3. Goals for next week
1. Continue working on the submitted ICCV 2022 paper for possible submission to the journal, Neurocomputing
https://www.journals.elsevier.com/neurocomputing
2. Provide actionable framework to the Contrastive Coding Cilia paper
- **Participants:**
- Blessing
- Shannon
- **Host:** Shannon
:::
:arrows_counterclockwise: Follow-up from June 17
---
Were any of these done? If so, check them off as you complete them.
**NO CHECKLIST ADDED LAST WEEK.**
- [Review the Feb 28 meeting notes](https://hackmd.io/vaxcrC_STXm3uE5Op49okQ#-Responsibilities) for core QRG postdoc responsibilities
- **Regular updates** on progress. This takes many forms:
- GitHub issues: creating new ones, closing old ones, updating open ones
- Pushing code to GitHub (ideally linking it to open issues)
- **Updating the weekly hackmd notes with your progress** (that's why we're doing this!)
- Engagement in Slack
- Weekly 1:1s
1. Set clear and unambiguous goals
2. Lay out **in detail** how those goals will be achieved and what key steps need to be hit along the way
3. Provide **regular updates** on your progress (GitHub, hackmd, Slack, zoom)
**No code pushes to GitHub. No GitHub issues updated. No discussions started or participated in on Slack. No goals, no details, NO UPDATES in the past week.**
:red_circle: Milestones
---
**What are our current goals?**
- [ICCV 2022](https://waset.org/computer-vision-conference-in-september-2022-in-vancouver) paper (SciPy topic, with some modified methods (???))
- Contrastive coding cilia segmentation ([ICML 2023](https://icml.cc/Conferences/FutureMeetings), January 2023 deadline; [MICCAI 2023](http://www.miccai.org/events/upcoming-conferences/), Feb-Mar 2023 deadline)
**What blockers to these goals exist?**
**Outline all possible details toward achieving these goals.**
**Provide a timeline toward achieving these goals.**
:dart: Goals for next week
---
- [ ] **Blessing**: a full draft of the ICCV paper
- Some experiments that still need to be run
- What are they?
- Experiments on fine segmentation
- experiments on evaluation metrics
- What code needs to be written?
- evaluation metrics
- fine segmentation on skeletonized mitochondrial images
- How will they be measured and assessed?
- they'll be measured against the study objectives and reults from literature
- How are they motivated? Why are they needed?
- The study was inspired by the recent work of Lefebvre et al., and the motivation
- originates from the need to deepen the ongoing inquiry into various automated image analysis
- tools for object detection and segmentationin.
- Sections of the paper still need to be written
- Experiments and results
- This would be completed on Sunday, June 26
- Explanation of new methods (and background of older ones)
- This would be completed on Sunday, June 26
- Motivation for why you pursued this new method(s)
- This would be completed by Monday, June 27
-
- How does MitoMeter fit in? Code, methods, etc?
- Similarities in dataset pre-processing, binarization and segmentation stages
## Notes
<!-- Other important details discussed during the meeting can be entered here. -->
---
:::info
- **Date:** June 17, 2022, 10:00am
- **Agenda**
1. Follow up from May 27
2. Reiteration of responsibilities
3. Milestones review
4. Goals for next week
- **Participants:**
- Blessing
- Shannon
- **Host:** Shannon
:::
:arrows_counterclockwise: Follow-up from May 27
---
Were any of these done? If so, **check them off as you complete them.**
**Put your checklist here.**
:heavy_check_mark: Reiteration of Responsibilities
---
- [Review the Feb 28 meeting notes](https://hackmd.io/vaxcrC_STXm3uE5Op49okQ#-Responsibilities) for core QRG postdoc responsibilities
- **Regular updates** on progress. This takes many forms:
- GitHub issues: creating new ones, closing old ones, updating open ones
- Pushing code to GitHub (ideally linking it to open issues)
- **Updating the weekly hackmd notes with your progress** (that's why we're doing this!)
- Engagement in Slack
- Weekly 1:1s
1. Set clear and unambiguous goals
2. Lay out **in detail** how those goals will be achieved and what key steps need to be hit along the way
3. Provide **regular updates** on your progress (GitHub, hackmd, Slack, zoom)
:red_circle: Milestones
---
**What are our current goals?**
- [ICCV 2022](https://waset.org/computer-vision-conference-in-september-2022-in-vancouver) paper (SciPy topic, with some modified methods (???))
- Contrastive coding cilia segmentation ([ICML 2023](https://icml.cc/Conferences/FutureMeetings), January 2023 deadline; [MICCAI 2023](http://www.miccai.org/events/upcoming-conferences/), Feb-Mar 2023 deadline)
**What blockers to these goals exist?**
**Outline all possible details toward achieving these goals.**
**Provide a timeline toward achieving these goals.**
:dart: Goals for next week
---
- [ ] **Blessing**: a full draft of the ICCV paper
- Some experiments that still need to be run
- What are they?
- What code needs to be written?
- How will they be measured and assessed?
- How are they motivated? Why are they needed?
- Sections of the paper still need to be written
- Experiments and results
- Explanation of new methods (and background of older ones)
- Motivation for why you pursued this new method(s)
- How does MitoMeter fit in? Code, methods, etc?
- [ ] **Shannon**: Create a Performance Improvement Plan
## Notes
<!-- Other important details discussed during the meeting can be entered here. -->
---
:::info
- **Date:** May 27, 2022, 10:00am
- **Agenda**
1. Follow up from last week
2. Milestone Review
3. Goals for next week
- **Participants:**
- Blessing
- Shannon
- **Host:** Shannon
:::
:arrows_counterclockwise: Follow-up from May 20
---
Were any of these done? If so, **check them off as you complete them.**
- [x] **Search for potential publication venues and put their URLs below**
- [ ] **Identify driver script and overall program architecture for MitoMeter**
- [ ] Open a pull request and set up the checklist of what needs to be done
- [ ] draft mode for PRs
- [ ] post issues related to code
- [ ] Remake bibtex file for cilia review paper as Mendeley currently seems to be generating a proprietary binary format that is unreadable by Overleaf
- [x] Post GitHub tickets/issues when you run into problems (**0 tickets posted this past week**)
- [ ] Run dataset through a diffuse background subtraction algorithm to remove noise between adjacent mitochondria
- [ ] Create a mask of the segmented mitochondria
:red_circle: Milestones
---
:dart: Goals for next week
---
## Notes
<!-- Other important details discussed during the meeting can be entered here. -->
Wasn't able to obtain videos but was able to obtain _frames_
- How?
-
---
:::info
- **Date:** May 20, 2022, 10:00am
- **Agenda**
1. Follow up from last week
2. Milestone Review
3. Goals for next week
- **Participants:**
- Blessing
- Shannon
- **Host:** Shannon
:::
:arrows_counterclockwise: Follow-up from May 13
---
Were any of these done? If so, **check them off as you complete them.**
- [x] **Search for potential publication venues and put their URLs below**
- [ ] **Identify driver script and overall program architecture for MitoMeter**
- [ ] Open a pull request and set up the checklist of what needs to be done
- [ ] draft mode for PRs
- [ ] post issues related to code
- [ ] Remake bibtex file for cilia review paper as Mendeley currently seems to be generating a proprietary binary format that is unreadable by Overleaf
- [x] Post GitHub tickets/issues when you run into problems (**0 tickets posted this past week**)
- [ ] Run dataset through a diffuse background subtraction algorithm to remove noise between adjacent mitochondria
- [ ] Create a mask of the segmented mitochondria
:red_circle: Milestones
---
- Short term
- [x] Load original mitochondrial image dataset
- [ ] Run dataset through a diffuse background subtraction algorithm to remove noise between adjacent mitochondria (**6 May 2022**)
- [ ] Create a mask of the segmented mitochondria (**6 May 2022**)
- [ ] Validate the segmentation and tracking algorithms---- 13 May 2022
- [ ] Get complete first draft and discuss paper with QRG---13 May 2022
- [ ] Design a poster for conference------- 20 May 2022
- Long term
- SciPy conference submission: 27 May 2022
- Cilia review paper submission: 15 May 2022
- Mitochondria review paper submission: 30 May 2022
- Contrastive Coding paper submission: 30 September 2022
- **Venue? Timeline?**
- Mitochondria journal paper submission: 30 November 2022
- **Topic? Venue? Timeline?**
- Cilia journal paper submission: 31 January 2023
- **Topic? Venue? Timeline?**
- Expand SciPy paper
- Comparison of denoising algorithms
- Segmentation
:dart: Goals for next week
---
## Notes
<!-- Other important details discussed during the meeting can be entered here. -->
- Installed napari but ran into errors
- Which errors?
- Still having video viewing issues
- Commit messages
- Contrast [scipy roadmap repo logs](https://github.com/quinngroup/SciPy_Paper_Roadmap/commits/main) vs [qhub commit logs](https://github.com/Quansight/qhub/commits/main)
- ICML deadline July 1
- CVPR deadline Aug 1
- MICCAI deadline ?? (usually Jan-Feb)
---
:::info
- **Date:** May 13, 2022, 1:00pm
- **Agenda**
1. Follow up from two weeks ago
2. Milestone Review
3. Goals for next week
- **Participants:**
- Blessing
- Shannon
- **Host:** Shannon
:::
:arrows_counterclockwise: Follow-up from April 29
---
Were any of these done? If so, **check them off as you complete them.**
- [ ] **Search for potential publication venues and put their URLs below**
- [ ] **Identify driver script and overall program architecture for MitoMeter**
- [ ] Open a pull request and set up the checklist of what needs to be done
- [ ] draft mode for PRs
- [ ] post issues related to code
- [ ] Remake bibtex file for cilia review paper as Mendeley currently seems to be generating a proprietary binary format that is unreadable by Overleaf
- [ ] Post GitHub tickets/issues when you run into problems (**0 tickets posted this past week**)
- [ ] Run dataset through a diffuse background subtraction algorithm to remove noise between adjacent mitochondria
- [ ] Create a mask of the segmented mitochondria
:exclamation: Progress
---
- **Why is NO CODE being pushed to GitHub?**
- 6 commits total (1 by Meekail, 1 by Shannon)
- **This should be happening SEVERAL TIMES A DAY. There is NO EXCUSE for not committing code.**
- Bulk of code on GitHub consists of reading video files
- **Deadline is in 2 weeks for the complete paper, so the analysis should be complete in NO MORE THAN a week.**
:red_circle: Milestones
---
- Short term
- [x] Load original mitochondrial image dataset
- [ ] Run dataset through a diffuse background subtraction algorithm to remove noise between adjacent mitochondria (**6 May 2022**)
- [ ] Create a mask of the segmented mitochondria (**6 May 2022**)
- [ ] Validate the segmentation and tracking algorithms---- 13 May 2022
- [ ] Get complete first draft and discuss paper with QRG---13 May 2022
- [ ] Design a poster for conference------- 20 May 2022
- Long term
- SciPy conference submission: 27 May 2022
- Cilia review paper submission: 15 May 2022
- Mitochondria review paper submission: 30 May 2022
- Contrastive Coding paper submission: 30 September 2022
- **Venue? Timeline?**
- Mitochondria journal paper submission: 30 November 2022
- **Topic? Venue? Timeline?**
- Cilia journal paper submission: 31 January 2023
- **Topic? Venue? Timeline?**
- Expand SciPy paper
- Comparison of denoising algorithms
- Segmentation
:dart: Goals for next week
---
- [ ] Work with Rachel on running baseline experiments for her OrNet SciPy paper
## Notes
<!-- Other important details discussed during the meeting can be entered here. -->
---
:::info
- **Date:** April 29, 2022, 10:00am
- **Agenda**
1. Follow up from last week
2. Milestones
3. Goals for next week
- **Participants:**
- Blessing
- Shannon
- **Host:** Shannon
:::
:arrows_counterclockwise: Follow-up from last week
---
Were any of these done? If so, **check them off as you complete them.**
- [x] **Add links in Notes section below for VS Code / GitOps tutorials you have been taking or plan to take**
- [x] https://www.youtube.com/watch?v=8A4TsoXJOs8
- [x] https://www.youtube.com/watch?v=nT8KGYVurIU
- [x] https://www.youtube.com/watch?v=a_FLqX3vGR4
- [x] https://www.youtube.com/watch?v=VqCgcpAypFQ
- [x] https://www.youtube.com/watch?v=ORrELERGIHs
- [ ] **Search for potential publication venues and put their URLs below**
- [ ] **Identify driver script and overall program architecture for MitoMeter**
- [ ] Open a pull request and set up the checklist of what needs to be done
- [ ] draft mode for PRs
- [ ] post issues related to code
- [ ] Remake bibtex file for cilia review paper as Mendeley currently seems to be generating a proprietary binary format that is unreadable by Overleaf
- [x] Set up short-term milestones
- These should be **concrete** and **measurable** (meaning it's easy to assess success or failure)
- These should have **hard deadlines** (specific dates; e.g., first draft of SciPy paper is due **May 28**)
- SciPy conference paper roadmap
- [x] Lay out a longer-term roadmap covering goals for the remainder of the postdoc appointment
:red_circle: Milestones
---
- Short term
- Load original mitochondrial image dataset------Done
- Run dataset through a diffuse background subtraction algorithm to remove noise between adjacent mitochondria 6 May 2022
- Create a mask of the segmented mitochondria 6 May 2022
- Validate the segmentation and tracking algorithms---- 13 May 2022
- Get complete first draft and discuss paper with QRG---13 May 2022
- Design a poster for conference------- 20 May 2022
- Long term
- SciPy conference submission: 27 May 2022
- Cilia review paper submission: 15 May 2022
- Mitochondria review paper submission: 30 May 2022
- Contrastive Coding paper submission: 30 September 2022
- **Venue? Timeline?**
- Mitochondria journal paper submission: 30 November 2022
- **Topic? Venue? Timeline?**
- Cilia journal paper submission: 31 January 2023
- **Topic? Venue? Timeline?**
- Expand SciPy paper
- Comparison of denoising algorithms
- Segmentation
:dart: Goals for next week
---
- [ ] Post GitHub tickets/issues when you run into problems
- [ ] Run dataset through a diffuse background subtraction algorithm to remove noise between adjacent mitochondria
- [ ] Create a mask of the segmented mitochondria
## Notes
<!-- Other important details discussed during the meeting can be entered here. -->
---
:::info
- **Date:** April 22, 2022, 10:30am
- **Agenda**
1. Follow up from three weeks ago
2. Statement
3. Milestones
4. Goals for next week
- **Participants:**
- Blessing
- Shannon
- **Host:** Shannon
:::
:arrows_counterclockwise: Follow-up from three weeks ago
---
Were any of these done? If so, **check them off as you complete them.**
- [x] (Shannon) Get a new laptop for Blessing (contact CS office)
- [ ] **Add links in Notes section below for VS Code / GitOps tutorials you have been taking or plan to take**
- [ ] **Search for potential publication venues and put their URLs below**
- [ ] **Identify driver script and overall program architecture for MitoMeter**
- [ ] Open a pull request and set up the checklist of what needs to be done
- [ ] draft mode for PRs
- [ ] post issues related to code
- [ ] Remake bibtex file for cilia review paper as Mendeley currently seems to be generating a proprietary binary format that is unreadable by Overleaf
:bust_in_silhouette: Statement
---
We're a full year into the 2-year appointment. Products so far:
- two in-progress review paper drafts
- two abstracts (BII 2021, SciPy 2022)
Problems that existed in 2021 and which are ongoing:
- Communication (e.g., being stuck but not telling anyone)
- Basic troubleshooting (ssh, git access, zoom permissions, Python)
- No committed code, no algorithm prototypes, no theoretical investigations
- Minimal interaction with the cilia/ornet datasets
- Minimal interaction with students in the lab
**At the halfway point, the time for reviewing is long over. Specific milestones need to be hit at very specific times for this postdoctoral appointment to be considered successful.**
:red_circle: Milestones
---
### High Priority
- SciPy poster + paper
- **Read, understand, and translate** existing Matlab code
- **Test** Python re-implementation
- **Compare** Python re-implementation to Matlab code
- **Generate** figures replicating paper results
- **Create poster** and **write paper**
- Note **poster** and **paper** deadlines
- Unspecified segmentation paper
- Based on MICCAI contrastive coding? Based on CellGraph density/gravimetric clustering? **Need to decide on this direction soon**
- **Identify** potential publication venues / journals
- **Explore** cilia / ornet datasets to help develop segmentation hypothesis
- GitOps
- **Writing** and **committing** code
- **Interacting** with existing code
- `git` commands (or VSCode integrations)
- Command-line familiarity (`git`, `ssh`, `python`, etc)
- **Regularly update** the "to-do" items in HackMD and issues on GitHub
- Sense of urgency
- Not stress, but an understanding of **what needs to get done** and **how much time you have left to do it**
- **Radical reprioritization**
### Low Priority
- Review papers
- (These should have been completed within the first six to nine months)
- They are still a good exercise but not what will get you a tenure-track position; **novel**, **first-author** publications will, so that should be the priority.
:dart: Goals for next week
---
- [ ] Set up short-term milestones
- These should be **concrete** and **measurable** (meaning it's easy to assess success or failure)
- These should have **hard deadlines** (specific dates; e.g., first draft of SciPy paper is due **May 28**)
- [ ] Lay out a longer-term roadmap covering goals for the remainder of the postdoc appointment
- What are the major objectives you want to achieve?
- Roughly what timeframe should you expect to achieve them?
## Notes
<!-- Other important details discussed during the meeting can be entered here. -->
CVPR / ICML 2023 submissions instead of FASEB?
---
:::info
- **Date:** April 1, 2022, 10:00am
- **Agenda**
- Follow up from last week
- Goals for next week
- **Participants:**
- Blessing
- Shannon
- **Host:** Shannon
:::
:arrows_counterclockwise: Follow-up from last week
---
### Review goals
- **Add links in Notes section below for VS Code / GitOps tutorials you have been taking or plan to take**
- **Search for potential publication venues and put their URLs below**
- **Identify driver script and overall program architecture for MitoMeter**
- Open a pull request and set up the checklist of what needs to be done
- draft mode for PRs
None of these goals are complete, and will be carried over to next week.
### :page_facing_up: Papers
- Running into problems with bibliography (*what problems?*)
- Not all the references are on google scholar (?)
- Find references to replace them
:dart: Goals for next week
---
- [ ] (Shannon) Get a new laptop for Blessing (contact CS office)
- [x] (Shannon) Look into renewal documents for Blessing to submit to CS office
- [ ] **Add links in Notes section below for VS Code / GitOps tutorials you have been taking or plan to take**
- [ ] **Search for potential publication venues and put their URLs below**
- [ ] **Identify driver script and overall program architecture for MitoMeter**
- [ ] Open a pull request and set up the checklist of what needs to be done
- [ ] draft mode for PRs
- [ ] post issues related to code
- [ ] Remake bibtex file for cilia review paper as Mendeley currently seems to be generating a proprietary binary format that is unreadable by Overleaf
## Notes
<!-- Other important details discussed during the meeting can be entered here. -->
Overleaf = Latex
- so if you're searching for how to do something in Overleaf, perhaps instead search for how to do it in Latex
- Also, [TeX StackExchange](https://tex.stackexchange.com/) is your friend
- Generating citations in Latex https://libguides.usask.ca/c.php?g=218034&p=1446425
---
:::info
- **Date:** March 25, 2022, 10:00am
- **Agenda**
- Follow up from last week
- Core GitOps skills review
- Goals for next week
- **Participants:**
- Blessing
- Shannon
- Meekail
- **Host:** Shannon
:::
:arrows_counterclockwise: Follow-up from last week
---
### :page_facing_up: Papers
- Cilia review paper [Overleaf link](https://www.overleaf.com/6847758215bcbqfhydjkfc)
- Introduction section needs some formatting fixes (e.g. paragraph breaks)
- Mitochondria review paper
- SciPy roadmap
### :desktop_computer: Programming
- VS Code Tutorials
- Which ones?
- GitOps Tutorials
- OrNet
- Have you run the models?
- MitoMeter port for SciPy?
- Cilia
- Contrastive coding implementation?
:mag: Core GitOps Skills Assessment
---
Remember GitOps from our first meeting:
- [GitOps](https://about.gitlab.com/topics/gitops/)
- Team-based software development process
- Required knowledge:
- command line
- [git](https://git-scm.com/) versioning system
- GitHub (including [Issues](https://docs.github.com/en/issues/tracking-your-work-with-issues/about-issues), [Projects](https://docs.github.com/en/issues/organizing-your-work-with-project-boards/managing-project-boards/about-project-boards), [Pull Requests](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests), [Actions](https://docs.github.com/en/actions), and [Codespaces](https://github.com/features/codespaces))
- Some kind of development environment / IDE (recommended: [Visual Studio Code](https://code.visualstudio.com/))
Since then:
- no git commits
- a [single empty repository](https://github.com/ojemebo/Reimplementation-practice)
- no issues on any quinngroup repos
- no PRs submitted, reviewed, or otherwise discussed
Other concerns:
- knowledge of `git` and how it works seems weak
- knowledge of GitHub and how it works also seems weak
- no concrete evidence yet of any coding over the past year
**This is a *problem*.**
- git and GitHub are how we coordinate on projects
- there's more to research than git and GitHub but if you're not participating *at all* that is a problem
- already three weeks since SciPy submission; there should be some progress on Python port of MitoMeter, but where is it? what about contrastive coding port?
**Need to dedicate time to GitOps and GitLab Flow.**
:dart: Goals for next week
---
- [ ] **Add links in Notes section below for VS Code / GitOps tutorials you have been taking or plan to take**
- [ ] **Search for potential publication venues and put their URLs below**
- [ ] **Identify driver script and overall program architecture for MitoMeter**
- [ ] Open a pull request and set up the checklist of what needs to be done
- [ ] draft mode for PRs
## Notes
<!-- Other important details discussed during the meeting can be entered here. -->
Potential publication venues for review papers
- https://ieeeaccess.ieee.org/
- https://journals.plos.org/ploscompbiol/
- https://elifesciences.org/ (probably a stretch)
- IEEE or ACM
Bahaa's contrastive coding work https://github.com/quinngroup/contrastive-coding
Tutorials
MitoMeter
- GitHub repo https://github.com/aelefebv/Mitometer
- Paper https://www.nature.com/articles/s41592-021-01234-z
Mitochondria review paper draft circulated in early April
- submission ready by middle of April
---
:::info
- **Date:** March 18, 2022, 10:00am
- **Agenda**
- Follow up from two weeks ago
- Goals for next week
- **Participants:**
- Blessing
- Shannon
- **Host:** Shannon
:::
---
1. Follow-up from two weeks ago
-----a)Cilia lit review paper was ported to Overleaf for editing by members of QRG.
Chenxiao, Riyal, and Albert You sent in their reviewed papers
-----b)A new SciPy roadmap (takes of 03/21/2022) was adopted by every SciPy author.
https://docs.google.com/spreadsheets/d/1V2-ZHFq9p7cWinM5zsEi5reQ4v4xcBSdWjTibdGJs78/edit?usp=sharing
-----c)Getting comfortable using VS Code but more tutorials are needed
-----d)I now have access to OrNet data via logan.cs.uga.edu
-----e)Still need access to the raw data since my work is doing segmentation
-----f)started work on investigating Contrastive learning and Wavelet Transforms for cilia segmentation
3. Goals for the week of 03/21
-----a))Take more VS Code tutorials
-----b))Load raw Ornet dataset, build model, tune parameters and write introductory page
-----c))Conclude review and editing on Cilia review paper
-----d))Continue working on investigating Wavelet Transforms for cilia segmentation
-----e))Continue working on Mitochondria review paper
-----f))Continue working on Contrastive coding and Wavelet Transforms on cilia segmentation paper
## Notes
How to include figures and graphics in Overleaf https://www.overleaf.com/learn/latex/Inserting_Images
Timeline for SciPy 2022 paper reviews https://github.com/scipy-conference/scipy_proceedings#timeline-for-2022
---
:arrows_counterclockwise: Follow-up from last week
---
### Papers to reading group
Literature review for survey paper (see Notes below)
### Roadmap for SciPy
Document: https://docs.google.com/document/d/1yAbIJu7yqAGxlL_dGqNxOqIOylu9rYY6Jj7DNYBPZbQ/edit?usp=sharing
Set up workshop/meeting with other SciPy authors (see Notes below)
### VS Code Tutorials
Went thorugh a lot of tutorials (where?)
- VS Code setup
- assessing data
### Projects
Not much time for other projects (yet)
**Cilia**
- Wavelet transforms for cilia segmentation
- See [Weiwen's master's thesis](https://cobweb.cs.uga.edu/~squinn/articles/WeiwenXu_MS_thesis_FINAL.pdf) for general Fourier performance in segmentation
- [Contrastive coding based segmentation (MICCAI 2021)](https://www.dropbox.com/s/3f2etdngncmr3re/contrastive_paper_MICCAI2021.pdf?dl=0)
### Got asked to review for SciPy! :tada:
One of the papers is in QRG, unfortunately, so will have to say no
Other papers are fine!
:dart: Goals for next week
---
1. Get on PAWS-Secure wifi network
2. Set up SciPy roadmap workshop/meeting with all other authors
i. Set up follow-up meetings for each week's goals?
ii. e.g. writing session to work on 1-page intros
3. Reach out to Chenxiao to set up survey paper meeting
4. Investigate wavelet and contrastive-coding based segmentation approaches for cilia
5. Start looking at [MitoMeter](https://www.nature.com/articles/s41592-021-01234-z) port to Python (for SciPy)
## Notes
<!-- Other important details discussed during the meeting can be entered here. -->
Great job sending out review paper and soliciting help
- Chenxiao volunteered! Start coordinating with her on it
- Needs to be a bit more _intentional_ (i.e., can't just paste the doc, ask for help, and expect volunteers)
- Put some time into reaching out to people and explaining why/how they can get involved
- Next step: **follow-up**
- Ping specific people
- Set up agendas for the meetings/workshops
---
###### tags: `Templates` `Meeting`
:::info
- **Date:** Feb 25, 2022, 10:00am
- **Agenda**
1. Go over self-review form
2. Responsibilities
- Mentoring
- Cilia Project
- OrNet Project
3. Expectations
- Literature
- Machine learning, computer vision, deep learning
- GitOps
- Python
4. Goals for next week
- **Participants:**
- Blessing
- Shannon
- **Host:** Shannon
:::
:books: Responsibilities
---
### Mentoring
- running project meetings
- _participating_ in project meetings
- collaborating with lab members
### Cilia Project ([summary](https://quinngroup.github.io/nsf-career.html))
- Build a quantitative vocabulary of ciliary motion (**[:rocket: mission statement](https://docs.google.com/document/d/16EfZKMi0jdJq_YiQNFyGT8tV5hHmt_Mz5SF9jWBDHeU/)**)
- Automated segmentation
- Motion representation
- Open source and web development
### OrNet Project
- Dynamic network representation of mitochondrial dynamics
- Automated segmentation
- [Mitometer](https://www.nature.com/articles/s41592-021-01234-z)?
- [HDBSCAN-based](https://hdbscan.readthedocs.io/en/latest/how_hdbscan_works.html) method?
- Graph neural network (GNN) for representation learning (Marcus)
:mag: Expectations
---
### Time/effort breakdown
- Cilia: 60% (3 days/week)
- OrNet: 30% (1.5 days/week)
- Mentoring: 10% (0.5 days/week)
### Mentoring
- Regular engagement with students
- Every research effort / paper should be in collaboration
- SciPy abstract was submitted with just your name and mine; that shouldn't happen
- Reading the same papers that the group reads
- Assigning students to review a paper with you
- Participating in meetings
- **Asking questions when you don't understand something**
### Literature
- Cilia and organellar networks background
- Machine learning, computer vision, deep learning
### Cilia project
- **Primary Research Objective**: Automated segmentation
- **Potential collaborators**:
- Meekail
- [Contrastive coding based segmentation (MICCAI 2021)](https://www.dropbox.com/s/3f2etdngncmr3re/contrastive_paper_MICCAI2021.pdf?dl=0)
- Mojtaba (available on Slack)
- Alireza (built the napari front-end)
- Chenxiao (working on wet lab end but has done basic non-ML and non-DL segmentation)
- Delaney, Victoria, and Sara (undergrads)
### OrNet project
- **Primary Research Objective**: Automated segmentation
- [Mitometer](https://www.nature.com/articles/s41592-021-01234-z)
- [Laniakea](https://www.nature.com/articles/nature13674) (or HDBSCAN-based gravimetric clustering)
- **Potential collaborators**:
- Meekail
- Rachel (Marcus too but he is focused on thesis)
- Delaney, Victoria, and Sara (undergrads)
### [GitOps](https://about.gitlab.com/topics/gitops/)
- Team-based software development process
- Required knowledge:
- command line
- [git](https://git-scm.com/) versioning system
- GitHub (including [Issues](https://docs.github.com/en/issues/tracking-your-work-with-issues/about-issues), [Projects](https://docs.github.com/en/issues/organizing-your-work-with-project-boards/managing-project-boards/about-project-boards), [Pull Requests](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests), [Actions](https://docs.github.com/en/actions), and [Codespaces](https://github.com/features/codespaces))
- Some kind of development environment / IDE (recommended: [Visual Studio Code](https://code.visualstudio.com/))
### [GitLab Flow](https://docs.gitlab.com/ee/topics/gitlab_flow.html)
- The process by which all the items in GitOps are marshalled and used throughout the software development process
- Focus on branching / merging / pull requests in git and GitHub to organize development
### Python
- Familiarity with PyData stack
- SciPy
- NumPy
- scikit-learn
- scikit-image
- OpenCV
- [conda](https://www.anaconda.com/products/individual) / [mamba](https://mamba.readthedocs.io/en/latest/)
- PyTorch
:dart: Goals for next week
---
- Send out papers to reading group
- 9-week roadmap for SciPy
- What needs to happen? What code needs to be written? What tests need to be built? What experiments need to be run?
- Go through more VS Code tutorials
- Jupyter notebooks on VS Code
- Sync up settings with GitHub Codespaces? ([quinngroup repositories](https://github.com/quinngroup/) are set up to use Codespaces)
## Notes
<!-- Other important details discussed during the meeting can be entered here. -->
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