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jcass11 merged 2 commits into from
Dec 10, 2024
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Fix typo in readme #57

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8ef809b
fix typo
jcass11 Dec 9, 2024
82147b0
add new supp fig s10 TFE example links
jcass11 Dec 10, 2024
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2 changes: 1 addition & 1 deletion README.md
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@@ -1,5 +1,5 @@
# Colony context and size-dependent compensation mechanisms give rise to variations in nuclear growth trajectories
The `dev` branch reflects the most up to date version of this analysis. To exactly reproduce the analysis as seen in bioRxiv manuscript use the `bioRxiv-v1`.
The `dev` branch reflects the most up to date version of this analysis. To exactly reproduce the analysis as seen in bioRxiv manuscript use the `bioRxiv-v1` branch.

The code in this repository generates all of the figures for Dixon et al. 2024 [(bioRxiv)](https://www.biorxiv.org/content/10.1101/2024.06.28.601071v1). It is primarily intended to support reproducibility of our research. In addition, researchers may find parts of this code valuable for future work.

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9 changes: 8 additions & 1 deletion docs/TFE_links.md
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Expand Up @@ -27,4 +27,11 @@ To explore the results and features generated by repository and shown in the pap
|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)|
|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)|
|S10A|Red example|Example volume trajectories with coordinated dips|[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&track=71044&t=53&filters=growth_outlier_filter%3A%3A3%2Cbaseline_colonies_dataset_filter%3A%3A3%2Cfullinterphase_dataset_filter%3A%3A3%2Clineageannotated_dataset_filter%3A%3A3&color=matplotlib-cool&palette-key=adobe&bg-sat=100&bg-brightness=100&fg-alpha=50&outlier-color=c0c0c0&outlier-mode=1&filter-color=dddddd&filter-mode=1&outline-color=ff00ff&tab=track_plot&bg=0&scalebar=1&timestamp=1&path=1&keep-range=0&scatter-range=all)|
|S10A|Blue example|Example volume trajectories with coordinated dips|[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&track=71675&t=44&filters=growth_outlier_filter%3A%3A3%2Cbaseline_colonies_dataset_filter%3A%3A3%2Cfullinterphase_dataset_filter%3A%3A3%2Clineageannotated_dataset_filter%3A%3A3&color=matplotlib-cool&palette-key=adobe&bg-sat=100&bg-brightness=100&fg-alpha=50&outlier-color=c0c0c0&outlier-mode=1&filter-color=dddddd&filter-mode=1&outline-color=ff00ff&tab=track_plot&bg=0&scalebar=1&timestamp=1&path=1&keep-range=0&scatter-range=all)|
|S10A|Green example|Example volume trajectories with coordinated dips|[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&track=75006&t=97&filters=growth_outlier_filter%3A%3A3%2Cbaseline_colonies_dataset_filter%3A%3A3%2Cfullinterphase_dataset_filter%3A%3A3%2Clineageannotated_dataset_filter%3A%3A3&color=matplotlib-cool&palette-key=adobe&bg-sat=100&bg-brightness=100&fg-alpha=50&outlier-color=c0c0c0&outlier-mode=1&filter-color=dddddd&filter-mode=1&outline-color=ff00ff&tab=track_plot&bg=0&scalebar=1&timestamp=1&path=1&keep-range=0&scatter-range=all)|
|S10A|Yellow example|Example volume trajectories with coordinated dips|[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&track=75725&t=155&filters=growth_outlier_filter%3A%3A3%2Cbaseline_colonies_dataset_filter%3A%3A3%2Cfullinterphase_dataset_filter%3A%3A3%2Clineageannotated_dataset_filter%3A%3A3&color=matplotlib-cool&palette-key=adobe&bg-sat=100&bg-brightness=100&fg-alpha=50&outlier-color=c0c0c0&outlier-mode=1&filter-color=dddddd&filter-mode=1&outline-color=ff00ff&tab=track_plot&bg=0&scalebar=1&timestamp=1&path=1&keep-range=0&scatter-range=all)|
|S10A|Orange example|Example volume trajectories with coordinated dips|[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&track=71915&t=207&filters=growth_outlier_filter%3A%3A3%2Cbaseline_colonies_dataset_filter%3A%3A3%2Cfullinterphase_dataset_filter%3A%3A3%2Clineageannotated_dataset_filter%3A%3A3&color=matplotlib-cool&palette-key=adobe&bg-sat=100&bg-brightness=100&fg-alpha=50&outlier-color=c0c0c0&outlier-mode=1&filter-color=dddddd&filter-mode=1&outline-color=ff00ff&tab=track_plot&bg=0&scalebar=1&timestamp=1&path=1&keep-range=0&scatter-range=all)|
|S10C||Example neighborhood of nuclei with coordinated volume dips|[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=change_in_volume_in_25_minute_window&t=239&filters=growth_outlier_filter%3A%3A3%2Cbaseline_colonies_dataset_filter%3A%3A3%2Cfullinterphase_dataset_filter%3A%3A3%2Clineageannotated_dataset_filter%3A%3A3&range=-200%2C200&color=matplotlib-purple_orange&palette-key=adobe&bg-sat=100&bg-brightness=100&fg-alpha=50&outlier-color=c0c0c0&outlier-mode=1&filter-color=dddddd&filter-mode=1&outline-color=ff00ff&tab=scatter_plot&bg=0&scalebar=1&timestamp=1&path=1&keep-range=0&bg-key=max_intensity_zprojection_of_lamin_b1&scatter-range=all&scatter-x=scatterplot_time&scatter-y=change_in_volume_in_25_minute_window)|

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