Reproduce all ipynb files of Dynamo 1

[Starlitnightly]

Conventional scRNA-seq

• [x] notebooks/zebrafish
• [x] notebooks/zebrafish_topography_analysis_tutorial

Differential geometry

• [x] notebooks/tutorial_hsc_dynamo_megakaryocytes_appearance
• [x] notebooks/tutorial_hsc_dynamo_cellwise_analysis
• [x] notebooks/tutorial_hsc_dynamo_basophil_lineage
• [x] notebooks/Differential_geometry

Labeling scRNA-seq

• [x] notebooks/scNT_seq_readthedocs
• [x] notebooks/tutorial_hsc_velocity
• [x] notebooks/scEU_seq_organoid_analysis_kinetic
• [x] notebooks/scEU_seq_rpe1_analysis_kinetic

Preprocessing

• [x] notebooks/tutorial_preprocess

Vector field predictions

• [ ] notebooks/lap_tutorial
• [x] notebooks/perturbation_tutorial