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chantelleleveille merged 3 commits into from
Nov 20, 2024
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Table with Fig TFE Links #38

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4 changes: 4 additions & 0 deletions README.md
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Expand Up @@ -70,3 +70,7 @@ python nuc_morph_analysis/lib/preprocessing/generate_perturbation_manifest.py
```bash
python nuc_morph_analysis/lib/visualization/write_data_for_colorizer.py
```

## Explore results in timelapse feature explorer

To interactively explore the results and features generated in this repository and shown in each figure panel of the paper follow the links provided in [this table](/docs/TFE_links.md).
30 changes: 30 additions & 0 deletions docs/TFE_links.md
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# Timelapse feature explorer links for data shown in figures

[Timelapse Feature Explorer](https://timelapse.allencell.org/) is a web-based tool that allows users to view timelapse segmentations with interactive and customizable colorization mapped according to relative intensities of quantitative features. In this viewer, nuclear segmentations from each individual colony timelapse are colorized by a chosen feature, with each nucleus in each frame being colored by its feature value in that frame. The resulting timelapses demonstrate how growth and shape features vary for all nuclei across the colony and over time, allowing for a qualitative assessment of spatiotemoral variation of these features. The tool also allows for selection of single nuclear trajectories, to visualize how individuals behave over time and compare to the population.

To explore the results and features generated by repository and shown in each figure panel of the paper Dixon et al. 2024 [(bioRxiv)](https://www.biorxiv.org/content/10.1101/2024.06.28.601071v1) follow the links in the table below.

|Figure|Subset of data relative to figure|Description|Timelapse feature explorer link|
|---|---|---|---|
|1E, 1F, S19|-|Example nucleus for segmentation (1E), formation/breakdown (1F) and transition point (S19) figures|[TFE link](https://timelapse.allencell.org/viewer?collection=https%3A%2F%2Fallencell.s3.amazonaws.com%2Faics%2Fnuc-morph-dataset%2Ftimelapse_feature_explorer_datasets%2Fbaseline_colonies_dataset%2Fcollection.json&dataset=Medium&feature=volume&track=83322&t=4&color=matplotlib-cool&palette-key=adobe&bg-sat=100&bg-brightness=100&fg-alpha=100&outlier-color=c0c0c0&outlier-mode=1&filter-color=dddddd&filter-mode=1&tab=track_plot&scalebar=1&timestamp=1&path=1&keep-range=0&scatter-range=all)|
|2A|-|Medium colony, height|[TFE link](https://timelapse.allencell.org/viewer?collection=https%3A%2F%2Fallencell.s3.amazonaws.com%2Faics%2Fnuc-morph-dataset%2Ftimelapse_feature_explorer_datasets%2Fbaseline_colonies_dataset%2Fcollection.json&dataset=Medium&feature=height&t=4&range=4%2C11&color=matplotlib-cool&palette-key=adobe&bg-sat=100&bg-brightness=100&fg-alpha=100&outlier-color=c0c0c0&outlier-mode=1&filter-color=dddddd&filter-mode=1&tab=scatter_plot&scalebar=1&timestamp=1&path=1&keep-range=0&scatter-range=all&scatter-x=scatterplot_time&scatter-y=height)|
|2B|-|Medium colony, volume with example highlighted|[TFE link](https://timelapse.allencell.org/viewer?collection=https%3A%2F%2Fallencell.s3.amazonaws.com%2Faics%2Fnuc-morph-dataset%2Ftimelapse_feature_explorer_datasets%2Fbaseline_colonies_dataset%2Fcollection.json&dataset=Medium&feature=volume&track=87165&t=4&range=400%2C1200&color=matplotlib-cool&palette-key=adobe&bg-sat=100&bg-brightness=100&fg-alpha=100&outlier-color=c0c0c0&outlier-mode=1&filter-color=dddddd&filter-mode=1&tab=track_plot&scalebar=1&timestamp=1&path=1&keep-range=0&scatter-range=all&scatter-x=scatterplot_time&scatter-y=volume)|
|2C|-|Medium colony, XY aspect raito with example 1 highlighted|[TFE link](https://timelapse.allencell.org/viewer?collection=https%3A%2F%2Fallencell.s3.amazonaws.com%2Faics%2Fnuc-morph-dataset%2Ftimelapse_feature_explorer_datasets%2Fbaseline_colonies_dataset%2Fcollection.json&dataset=Medium&feature=xy_aspect_ratio&track=83321&t=23&range=1%2C2.500&color=matplotlib-cool&palette-key=adobe&bg-sat=100&bg-brightness=100&fg-alpha=100&outlier-color=c0c0c0&outlier-mode=1&filter-color=dddddd&filter-mode=1&tab=track_plot&scalebar=1&timestamp=1&path=1&keep-range=0&scatter-range=all&scatter-x=scatterplot_time&scatter-y=volume)|
|2C|-|Medium colony, XY aspect ratio with example 2 highlighted|[TFE link](https://timelapse.allencell.org/viewer?collection=https%3A%2F%2Fallencell.s3.amazonaws.com%2Faics%2Fnuc-morph-dataset%2Ftimelapse_feature_explorer_datasets%2Fbaseline_colonies_dataset%2Fcollection.json&dataset=Medium&feature=xy_aspect_ratio&track=87094&t=23&range=1%2C2.500&color=matplotlib-cool&palette-key=adobe&bg-sat=100&bg-brightness=100&fg-alpha=100&outlier-color=c0c0c0&outlier-mode=1&filter-color=dddddd&filter-mode=1&tab=track_plot&scalebar=1&timestamp=1&path=1&keep-range=0&scatter-range=all&scatter-x=scatterplot_time&scatter-y=volume)|
|3A top|-|Small colony, height|[TFE link](https://timelapse.allencell.org/viewer?collection=https%3A%2F%2Fallencell.s3.amazonaws.com%2Faics%2Fnuc-morph-dataset%2Ftimelapse_feature_explorer_datasets%2Fbaseline_colonies_dataset%2Fcollection.json&dataset=Small&feature=height&range=4%2C11&color=matplotlib-cool&palette-key=adobe&bg-sat=100&bg-brightness=100&fg-alpha=100&outlier-color=c0c0c0&outlier-mode=1&filter-color=dddddd&filter-mode=1&tab=scatter_plot&scalebar=1&timestamp=1&path=1&keep-range=1&scatter-range=all&scatter-x=scatterplot_time&scatter-y=height)|
|3A middle|-|Medium colony, height|[TFE link](https://timelapse.allencell.org/viewer?collection=https%3A%2F%2Fallencell.s3.amazonaws.com%2Faics%2Fnuc-morph-dataset%2Ftimelapse_feature_explorer_datasets%2Fbaseline_colonies_dataset%2Fcollection.json&dataset=Medium&feature=height&range=4%2C11&color=matplotlib-cool&palette-key=adobe&bg-sat=100&bg-brightness=100&fg-alpha=100&outlier-color=c0c0c0&outlier-mode=1&filter-color=dddddd&filter-mode=1&tab=scatter_plot&scalebar=1&timestamp=1&path=1&keep-range=0&scatter-range=all&scatter-x=scatterplot_time&scatter-y=height)|
|3A bottom|-|Large colony, height|[TFE link](https://timelapse.allencell.org/viewer?collection=https%3A%2F%2Fallencell.s3.amazonaws.com%2Faics%2Fnuc-morph-dataset%2Ftimelapse_feature_explorer_datasets%2Fbaseline_colonies_dataset%2Fcollection.json&dataset=Large&feature=height&range=4%2C11&color=matplotlib-cool&palette-key=adobe&bg-sat=100&bg-brightness=100&fg-alpha=100&outlier-color=c0c0c0&outlier-mode=1&filter-color=dddddd&filter-mode=1&tab=scatter_plot&scalebar=1&timestamp=1&path=1&keep-range=1&scatter-range=all&scatter-x=scatterplot_time&scatter-y=height)|
|3C|-|Medium colony, normalized distance from colony center|[TFE link](https://timelapse.allencell.org/viewer?collection=https%3A%2F%2Fallencell.s3.amazonaws.com%2Faics%2Fnuc-morph-dataset%2Ftimelapse_feature_explorer_datasets%2Fbaseline_colonies_dataset%2Fcollection.json&dataset=Medium&feature=normalized_distance_from_colony_center&color=matplotlib-viridis&palette-key=adobe&bg-sat=100&bg-brightness=100&fg-alpha=100&outlier-color=c0c0c0&outlier-mode=1&filter-color=dddddd&filter-mode=1&tab=scatter_plot&scalebar=1&timestamp=1&path=1&keep-range=0&scatter-range=all&scatter-x=scatterplot_time&scatter-y=height)|
|4A, 4B|Small colony data|Full-interphase volume trajectories|[TFE link](https://timelapse.allencell.org/viewer?collection=https%3A%2F%2Fallencell.s3.amazonaws.com%2Faics%2Fnuc-morph-dataset%2Ftimelapse_feature_explorer_datasets%2Ffull-interphase_dataset%2Fcollection.json&dataset=Small&feature=volume&t=4&color=matplotlib-cool&palette-key=adobe&bg-sat=100&bg-brightness=100&fg-alpha=100&outlier-color=c0c0c0&outlier-mode=1&filter-color=dddddd&filter-mode=1&tab=scatter_plot&scalebar=1&timestamp=1&path=1&keep-range=0&scatter-range=all&scatter-x=synchronized_time&scatter-y=volume)|
|4A, 4B|Medium colony data|Full-interphase volume trajectories|[TFE link](https://timelapse.allencell.org/viewer?collection=https%3A%2F%2Fallencell.s3.amazonaws.com%2Faics%2Fnuc-morph-dataset%2Ftimelapse_feature_explorer_datasets%2Ffull-interphase_dataset%2Fcollection.json&dataset=Medium&feature=volume&t=4&color=matplotlib-cool&palette-key=adobe&bg-sat=100&bg-brightness=100&fg-alpha=100&outlier-color=c0c0c0&outlier-mode=1&filter-color=dddddd&filter-mode=1&tab=scatter_plot&scalebar=1&timestamp=1&path=1&keep-range=0&scatter-range=all&scatter-x=synchronized_time&scatter-y=volume)|
|4A, 4B|Large colony data|Full-interphase volume trajectories|[TFE link](https://timelapse.allencell.org/viewer?collection=https%3A%2F%2Fallencell.s3.amazonaws.com%2Faics%2Fnuc-morph-dataset%2Ftimelapse_feature_explorer_datasets%2Ffull-interphase_dataset%2Fcollection.json&dataset=Large&feature=volume&t=4&color=matplotlib-cool&palette-key=adobe&bg-sat=100&bg-brightness=100&fg-alpha=100&outlier-color=c0c0c0&outlier-mode=1&filter-color=dddddd&filter-mode=1&tab=scatter_plot&scalebar=1&timestamp=1&path=1&keep-range=0&scatter-range=all&scatter-x=synchronized_time&scatter-y=volume)|
|4C|-|Example volume trajectory|[TFE link](https://timelapse.allencell.org/viewer?collection=https%3A%2F%2Fallencell.s3.amazonaws.com%2Faics%2Fnuc-morph-dataset%2Ftimelapse_feature_explorer_datasets%2Ffull-interphase_dataset%2Fcollection.json&dataset=Medium&feature=volume&track=83322&t=4&color=matplotlib-cool&palette-key=adobe&bg-sat=100&bg-brightness=100&fg-alpha=100&outlier-color=c0c0c0&outlier-mode=1&filter-color=dddddd&filter-mode=1&tab=track_plot&scalebar=1&timestamp=1&path=1&keep-range=0&scatter-range=all)|
|5B left|-|Example super-linear trajectory|[TFE link](https://timelapse.allencell.org/viewer?collection=https%3A%2F%2Fallencell.s3.amazonaws.com%2Faics%2Fnuc-morph-dataset%2Ftimelapse_feature_explorer_datasets%2Ffull-interphase_dataset%2Fcollection.json&dataset=Small&feature=volume&track=76452&t=317&color=matplotlib-cool&palette-key=adobe&bg-sat=100&bg-brightness=100&fg-alpha=100&outlier-color=c0c0c0&outlier-mode=1&filter-color=dddddd&filter-mode=1&tab=track_plot&scalebar=1&timestamp=1&path=1&keep-range=0&scatter-range=all)|
|5B right|-|Example sub-linear trajectory|[TFE link](https://timelapse.allencell.org/viewer?collection=https%3A%2F%2Fallencell.s3.amazonaws.com%2Faics%2Fnuc-morph-dataset%2Ftimelapse_feature_explorer_datasets%2Ffull-interphase_dataset%2Fcollection.json&dataset=Small&feature=volume&track=74396&t=254&color=matplotlib-cool&palette-key=adobe&bg-sat=100&bg-brightness=100&fg-alpha=100&outlier-color=c0c0c0&outlier-mode=1&filter-color=dddddd&filter-mode=1&tab=track_plot&scalebar=1&timestamp=1&path=1&keep-range=0&scatter-range=all)|
|7B|-|Visualization of semgentations filtered to example lineage tree / Family ID|[TFE link](https://timelapse.allencell.org/viewer?collection=https%3A%2F%2Fallencell.s3.amazonaws.com%2Faics%2Fnuc-morph-dataset%2Ftimelapse_feature_explorer_datasets%2Fexploratory_dataset%2Fcollection.json&dataset=Medium&feature=family_id&filters=family_id%3A%3A42%3A42&range=42%2C42&color=matplotlib-cool&palette-key=adobe&bg-sat=100&bg-brightness=100&fg-alpha=100&outlier-color=c0c0c0&outlier-mode=1&filter-color=dddddd&filter-mode=1&tab=filters&scalebar=1&timestamp=1&path=1&keep-range=0&scatter-range=all&scatter-x=scatterplot_time&scatter-y=family_id)|
|S7A|Small colony data|Apoptotic nuclei (red trajectories in figure, plus additional apoptotic trajectories)|[TFE link](https://timelapse.allencell.org/viewer?collection=https%3A%2F%2Fallencell.s3.amazonaws.com%2Faics%2Fnuc-morph-dataset%2Ftimelapse_feature_explorer_datasets%2Fexploratory_dataset%2Fcollection.json&dataset=Small&feature=volume&t=374&filters=trajectory_termination_annotation%3A%3Affc&color=matplotlib-cool&palette-key=adobe&bg-sat=100&bg-brightness=100&fg-alpha=100&outlier-color=c0c0c0&outlier-mode=1&filter-color=dddddd&filter-mode=1&tab=scatter_plot&scalebar=1&timestamp=1&path=1&keep-range=0&scatter-range=all&scatter-x=scatterplot_time&scatter-y=volume)|
|S7A|Medium colony data|Apoptotic nuclei (red trajectories in figure, plus additional apoptotic trajectories)|[TFE link](https://timelapse.allencell.org/viewer?collection=https%3A%2F%2Fallencell.s3.amazonaws.com%2Faics%2Fnuc-morph-dataset%2Ftimelapse_feature_explorer_datasets%2Fexploratory_dataset%2Fcollection.json&dataset=Medium&feature=volume&t=174&filters=trajectory_termination_annotation%3A%3Affc&color=matplotlib-cool&palette-key=adobe&bg-sat=100&bg-brightness=100&fg-alpha=100&outlier-color=c0c0c0&outlier-mode=1&filter-color=dddddd&filter-mode=1&tab=scatter_plot&scalebar=1&timestamp=1&path=1&keep-range=0&scatter-range=all&scatter-x=scatterplot_time&scatter-y=volume)|
|S7A|Large colony data|Apoptotic nuclei (red trajectories in figure, plus additional apoptotic trajectories)|[TFE link](https://timelapse.allencell.org/viewer?collection=https%3A%2F%2Fallencell.s3.amazonaws.com%2Faics%2Fnuc-morph-dataset%2Ftimelapse_feature_explorer_datasets%2Fexploratory_dataset%2Fcollection.json&dataset=Large&feature=volume&t=237&filters=trajectory_termination_annotation%3A%3Affc&color=matplotlib-cool&palette-key=adobe&bg-sat=100&bg-brightness=100&fg-alpha=100&outlier-color=c0c0c0&outlier-mode=1&filter-color=dddddd&filter-mode=1&tab=scatter_plot&scalebar=1&timestamp=1&path=1&keep-range=0&scatter-range=all&scatter-x=scatterplot_time&scatter-y=volume)|
|S7A|Small colony data|Growth outliers (yellow and blue trajectories in figure)|[TFE link](https://timelapse.allencell.org/viewer?collection=https%3A%2F%2Fallencell.s3.amazonaws.com%2Faics%2Fnuc-morph-dataset%2Ftimelapse_feature_explorer_datasets%2Fexploratory_dataset%2Fcollection.json&dataset=Small&feature=volume&t=212&filters=growth_outlier_filter%3A%3A2&color=matplotlib-cool&palette-key=adobe&bg-sat=100&bg-brightness=100&fg-alpha=100&outlier-color=c0c0c0&outlier-mode=1&filter-color=dddddd&filter-mode=1&tab=scatter_plot&scalebar=1&timestamp=1&path=1&keep-range=0&scatter-range=all&scatter-x=scatterplot_time&scatter-y=volume)|
|S7A|Medium colony data|Growth outliers (yellow trajectories in figure)|[TFE link](https://timelapse.allencell.org/viewer?collection=https%3A%2F%2Fallencell.s3.amazonaws.com%2Faics%2Fnuc-morph-dataset%2Ftimelapse_feature_explorer_datasets%2Fexploratory_dataset%2Fcollection.json&dataset=Medium&feature=volume&t=212&filters=growth_outlier_filter%3A%3A2&color=matplotlib-cool&palette-key=adobe&bg-sat=100&bg-brightness=100&fg-alpha=100&outlier-color=c0c0c0&outlier-mode=1&filter-color=dddddd&filter-mode=1&tab=scatter_plot&scalebar=1&timestamp=1&path=1&keep-range=0&scatter-range=all&scatter-x=scatterplot_time&scatter-y=volume)|
|S7A|Large colony data|Growth outliers (yellow trajectories in figure)|[TFE link](https://timelapse.allencell.org/viewer?collection=https%3A%2F%2Fallencell.s3.amazonaws.com%2Faics%2Fnuc-morph-dataset%2Ftimelapse_feature_explorer_datasets%2Fexploratory_dataset%2Fcollection.json&dataset=Large&feature=volume&t=372&filters=growth_outlier_filter%3A%3A2&color=matplotlib-cool&palette-key=adobe&bg-sat=100&bg-brightness=100&fg-alpha=100&outlier-color=c0c0c0&outlier-mode=1&filter-color=dddddd&filter-mode=1&tab=scatter_plot&scalebar=1&timestamp=1&path=1&keep-range=0&scatter-range=all&scatter-x=scatterplot_time&scatter-y=volume)|