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Refactoring MSD, smoothness and dynamic range calculations and unecessary script cleanup #219

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Refactoring MSD, smoothness and dynamic range calculations and unecessary script cleanup #219

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edyoshikun
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@edyoshikun edyoshikun commented Jan 8, 2025 •
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This PR refactors and adds the calculations for:

  • Mean square displacement
  • Slope calculation for smoothness
  • Normalization strategies for the embeddings prior analysis Decided to use raw
  • Cleaning up unecessary/obsolete scripts

Soorya19Pradeep
Soorya19Pradeep reviewed Jan 8, 2025
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@edyoshikun edyoshikun changed the title Refactoring MSD, smoothness and dynamic range calculations Refactoring MSD, smoothness and dynamic range calculations and unecessary script cleanup Jan 10, 2025
edyoshikun and others added 26 commits April 23, 2025 17:52
@edyoshikun
plot pc video
dca68ab
@edyoshikun
adding plotting of conditions
95d76f7
@edyoshikun
saving clusters as json
76a9e09
@Soorya19Pradeep
sectioned code for two models
719c54d
@Soorya19Pradeep
Merge branch 'msd_update' of https://github.com/mehta-lab/VisCy into …
57f28c0 
…msd_update
@edyoshikun
pc exploration and update for cleaner condition saving
2fb3955
@Soorya19Pradeep
changed image save format
4e128fa
@Soorya19Pradeep
add script for imagenet model
6afe710
@Soorya19Pradeep
Merge branch 'msd_update' of https://github.com/mehta-lab/VisCy into …
6d881f3 
…msd_update
@edyoshikun
openphenom
9cca143
@Soorya19Pradeep
add phatemap plots with tracks
38fa395
@Soorya19Pradeep
add missing import
99a8055
@Soorya19Pradeep
black format scripts
3e24eed
@edyoshikun
adding alfi
836d52c
@edyoshikun
plotting tracks on phate
2064922
@Soorya19Pradeep
add msd plotting
8ac93ed
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save as svg
257ce40
@Soorya19Pradeep
fixed figure sizes
4666876
@edyoshikun
compute_pca refactoring
340dbc6
@edyoshikun
adding the openphenom features
576906c
@Soorya19Pradeep
split imagenet script for applications
1d9361d
@Soorya19Pradeep
move functions into utils
3ccf8cf
@Soorya19Pradeep
moved scripts to evaluation
b98f26f
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add pd read in metrics function
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@Soorya19Pradeep
black formated
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@edyoshikun
f1 score
39e4e71
@edyoshikun edyoshikun changed the base branch from main to dynaclr_v2 May 16, 2025 20:45
@ziw-liu
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ziw-liu commented May 23, 2025

@edyoshikun is this still intended to be merged?

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No, this branch is going to be closed in favor of #240

@edyoshikun edyoshikun closed this May 30, 2025
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