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Adding TArrow for testing #220

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This PR adds the Tarrow package wrapped with lightning. It also contains a DataLoader to get the pair of timepoints from ome-zarr.

edyoshikun and others added 26 commits January 7, 2025 18:10
@edyoshikun
updating the MSD calculation
25322e2
@edyoshikun
MSD with different normalizations and removing unecessary arguments
0fcb0e6
@edyoshikun
adding more paths from old code
091fabb
@edyoshikun
add log log plot and the slope
823c971
@edyoshikun
making a dictionary to plot easier
1ab24d2
@edyoshikun
simplify MSD.
310688e
@Soorya19Pradeep
add scaling and change to log plot
2e8d243
@edyoshikun
reverting and restricting to only euclidean
a63fe23
@edyoshikun
changing tau to delta_t and frames to seconds
b57b2cf
@Soorya19Pradeep
delete scratch scripts
915cc24
@Soorya19Pradeep
deleted duplicate scripts
efdcec0
@Soorya19Pradeep
deleted duplicate script
c2d1b3e
@Soorya19Pradeep
add accuracy metric plot
a530523
@Soorya19Pradeep
plot ALFI phatemap with annotation
83a4583
@Soorya19Pradeep
style plot
a090eb9
@edyoshikun
adding back cosine
e397de1
@edyoshikun
adding the normalization of the euclidian distance and the code for p…
fb93f60 
…lotting
@edyoshikun
cleanup and refactoring to move usefult functions into viscy.represen…
57851bc 
…tation.evaluation.distance and clustering files
@Soorya19Pradeep
changed csv file naming
1037893
@Soorya19Pradeep
add script for ALFI cell division
5a9c296
@edyoshikun
PCA analysis
4ecc79b
@edyoshikun
adding the random track sampling
8a2073b
@Soorya19Pradeep
add script for interactive plot with image display
d8fa880
@edyoshikun
gmm clustering and silhoutte score
8326788
@edyoshikun
fix the issue with distance.py for plotting the pairwise matrix
bf0bf1e
@edyoshikun
prototype wrapping the timearrow model and dataloader that takes ome-…
bec0de2 
…zarr to spit to tarrowdataset
ziw-liu
ziw-liu reviewed Jan 29, 2025
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@edyoshikun edyoshikun marked this pull request as draft January 29, 2025 23:18
@ziw-liu ziw-liu added enhancement New feature or request representation Representation learning (SSL) labels Jan 30, 2025
@edyoshikun edyoshikun marked this pull request as ready for review February 3, 2025 16:19
@edyoshikun edyoshikun requested a review from ziw-liu February 3, 2025 16:19
@mattersoflight mattersoflight self-requested a review February 4, 2025 15:46
mattersoflight
mattersoflight reviewed Feb 9, 2025
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viscy/data/tarrow.py Outdated
from tarrow.data.tarrow_dataset import TarrowDataset
from torch.utils.data import ConcatDataset, DataLoader

from viscy.utils.engine_state import set_fit_global_state
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viscy.utils.engine_state doesn't exist. Missing commit?

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@edyoshikun I was able to draw a batch and construct the model!
I now realize the model encodes temporal changes into a dense representation at each time point. The output tensor has 16 channels for each pixel in the input. In other words, the model "lifts" the image into a higher dimension instead of "compressing" it into an embedding.
image

For any meaningful comparison with dynaCLR, we will need a downstream embedding model:

image

@ziw-liu ziw-liu added this to the v0.4.0 milestone Mar 27, 2025
@edyoshikun edyoshikun changed the base branch from msd_update to main August 23, 2025 19:35
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@ziw-liu ziw-liu Awaiting requested review from ziw-liu

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enhancement New feature or request representation Representation learning (SSL)

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@edyoshikun @mattersoflight @ziw-liu @Soorya19Pradeep