---
# System prepended metadata

title: Toxo Meeting Minutes
tags: [Templates, Meeting]

---

Toxo Meeting Minutes
===

:::info
- **Date:** April 22, 2022, 1:00pm ET
- **Agenda**
1. Catch-up from April 8 meeting
2. Other updates
3. Goals for next meeting
- **Participants:**
    - Shannon
    - Gianni
    - Alireza
- **Host:** Shannon
:::

:books: Catch-up from April 8
---

 - Integration with napari
 - Trying more preprocessing methods
 - Try CellPose 2.0 model
 - Napari tracking plugins
 - Start writing?
     - Overleaf https://www.overleaf.com/4332759976qqbckvmbbmnn

Virtual poster
 - So definitely want something in a notebook / mybinder / napari format!

In particular:
- Silvia's paper (connection between spatial movement + fluorscence oscillation)
 - DSAA 2019 paper

Any movement here?

:bust_in_silhouette: Other updates
---

Alireza
 - No updates on Toxo
 - Some cluster work
 - A few interviews

Gianni
 - CellPose 2.0 is a little unclear
 - Start writing, learn more latex
 - Tutorials on napari


:dart: Goals for next meeting
---

 - Napari running
 - Preprocessing
 - Tracking + classification
 - CellPose 2.0 and compare to PlantSeg

## Notes 

Inserting figures in Overleaf https://www.overleaf.com/learn/latex/Inserting_Images

---

:::info
- **Date:** April 8, 2022, 1:00pm ET
- **Agenda**
1. Catch-up from Feb 11 (!) meeting
2. SciPy abstract
3. CellPose 2.0
4. Status of other papers
5. Goals for next meeting
- **Participants:**
    - Shannon
    - Gianni
    - Alireza
- **Host:** Shannon
:::

:books: Feb 11 meeting catch-up
---
 - Silvia + microscope resolution information [(Alireza answered)](/lTYTz1GwQkqI8NE2CiyoQw)
 - Pretty much did a parameter scan over all the options in PlantSeg
 - Getting "clairvoyant" segmentations: PlantSeg will identify a cell that doesn't appear, but then not identify it when it DOES appear deeper in the z-axis
 - Rethinking some of the preprocessing
     - Just a Gaussian filter seems to work reasonably well
 - Still getting under-segmentation (some predicted masks that incorporate multiple actual cells)

![](https://i.imgur.com/ubwzrKE.png)

 - Mojtaba hard-coded some aspect, tailored specifically to the 3D dataset
     - A lot of the de-noising took place during the reconstruction step
 - Make napari a front-end for PlantSeg

:snake: SciPy abstract
---
 
**Accepted!** :clap: 

Next steps?

Virtual poster
 - So definitely want something in a notebook / mybinder / napari format!

:microscope: CellPose 2.0
---

 - :newspaper: [Paper](https://www.biorxiv.org/content/10.1101/2022.04.01.486764v1)
 - :bird: [Twitter](https://twitter.com/marius10p/status/1511415409047650307?s=20&t=umTVIG1CFKIWHYMrQqFKyQ)
 - :spider_web: [Website](https://www.cellpose.org/)
Supposedly, version 2.0 not only makes training your own models easier (we do have supervised data!), but is also much better at anisotropic data. Might be worth a shot?

:writing_hand: Other papers
---
In particular:
- Silvia's paper (connection between spatial movement + fluorscence oscillation)
 - DSAA 2019 paper

Any movement here?

:dart: Goals for next meeting
---

 - Integration with napari
 - Trying more preprocessing methods
 - Try CellPose 2.0 model
 - Napari tracking plugins
 - Start writing?
     - Overleaf https://www.overleaf.com/4332759976qqbckvmbbmnn

:closed_book: Tasks
--
==Importance== (1 *most* - 5 *least*) / Task / **Estimate** (# of hours)



## Notes 

Funding flowchart for attending SciPy

![](https://i.imgur.com/R6ZAttp.png)

---


###### tags: `Templates` `Meeting`

:::info
- **Date:** Feb 11, 2022, 1:00pm ET
- **Agenda**
1. Catch-up from Feb 4 meeting
2. SciPy abstract
3. Other updates
- **Participants:**
    - Shannon
    - Gianni
    - Alireza
- **Host:** Shannon

:::

:books: Feb 4 meeting catch-up
---
 - PlantSeg strategies
 - CellPose
 - Mojtaba + cleaned 3D data
 - Silvia + microscope resolution information [(Alireza answered)](/lTYTz1GwQkqI8NE2CiyoQw)
 - Sparse deconv paper

:snake: SciPy abstract
---
 - https://docs.google.com/document/d/111LaBTtnMfwXMV7H01WFmUPf1VpWWDNQhoXSyzosZHI/edit?usp=sharing
 - [The final document I submitted](https://docs.google.com/document/d/19PSaDyk0G9MuuxyNX9Z83L3LM-p4HvJAuw9TaKrhe4Y/edit?usp=sharing)

:dart: Other updates
---
 - Napari plugin for toxo segmentation / tracking / phenotype classification
     - Convert the SciPy paper to this
     - Make a list of other major plugins available that kinda sorta do what ours does; we'll need to test some of these as part of our paper

## Goals for this week
 
 - Pull out preprocessing steps from 2018 code https://github.com/quinngroup/toxoplasma-3DTracking
     - Yeah, [this is definitely the preprocessing code](https://github.com/quinngroup/toxoplasma-3DTracking/blob/master/notebooks/3D_Tracking_detection_module.ipynb)
 - How much preprocessing is built into PlantSeg?
 ~~- Edit and submit SciPy abstract~~
     - Victoria has offered to edit!

:closed_book: Tasks
--
==Importance== (1 *most* - 5 *least*) / Task / **Estimate** (# of hours)

 - [x] ==2== Ask Silvia about microscope resolution / magnification, and see if perhaps she knows pixel size
 - [x] ==1== Start playing with PlantSeg, and in particular look into its preprocessing abilities
 - [x] ==1== Edit SciPy abstract to include napari plugin; staged analytics that includes swappable preprocessing; performance improvements from the 2018 proof of concept

## Notes 

 - One of the bigger problems in the [2018 3D paper was locality](https://github.com/osbd/osbd-2018/raw/master/proceedings/S09209_6003.pdf) 
     - Centroids used from frame to frame
     - Noisey centroids required filtering and additional processing

---

###### tags: `Templates` `Meeting`

:::info
- **Date:** Feb 4, 2022, 2:00pm ET
- **Agenda**
1. Catch-up from fall 2021
2. Plans for spring 2022
- **Participants:**
    - Shannon
    - Gianni
    - Alireza
- **Host:** Shannon

:::

:books: Fall 2021 Review
---
- Segmentation strategies using PlantSeg

:dart: Spring 2022 Goals
---
 - Graduate Gianni (May or August)!
 - Check out CellPose
 - Get a paper out
     - [JOSS](https://joss.theoj.org/)
     - Silvia's paper (connection between spatial movement + fluorscence oscillation)
     - DSAA 2019 paper
     - Computational methods for exploring spatial movement + fluorescence oscillation
     - [:heavy_check_mark:] SciPy paper https://www.scipy2022.scipy.org/talk-poster-presentations . Abstract deadline: Feb 22
 - Cleaning up images / noise in 3D images
 - Look into sparse convolutions

## Goals for this week
 
 - What kind of segmentation? is plantseg the way to go, or some other pre-packaged / pre-trained 3D segmentation?
 - Figure out a preprocessing pipeline
 - Start designing for JOSS submission
 - [:heavy_check_mark:] Draft for SciPy abstract (due Feb 11) [Google doc](https://docs.google.com/document/d/111LaBTtnMfwXMV7H01WFmUPf1VpWWDNQhoXSyzosZHI/edit?usp=sharing)

:closed_book: Tasks
--
==Importance== (1 *most* - 5 *least*) / Task / **Estimate** (# of hours)

 - [x] ==1== Find out if Mojtaba has an archive of the cleaned 3D data
     - Seems unlikely
 - [x] ==1== Start working on a SciPy abstract(s) to workshop next week [Google doc](https://docs.google.com/document/d/111LaBTtnMfwXMV7H01WFmUPf1VpWWDNQhoXSyzosZHI/edit?usp=sharing)
 - [ ] ==2== Ask Silvia about microscope resolution / magnification, and see if perhaps she knows pixel size
 - [ ] ==2== Read sparse deconv paper https://www.nature.com/articles/s41587-021-01092-2

## Notes 
<!-- Other important details discussed during the meeting can be entered here. -->

Meetings will normally be every other week on Fridays at 1pm

Idea of signal propagation across space and time
    - within a single time point (z-slices), find sources of fluorescence that persist in multiple consecutive z-slices
    - across multiple time points, find objects that persist across multiple consecutive time points
    
