Toxo Meeting Minutes

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  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