Illustration of the visualization of datasets of various complexity and nature in the MorphoNet standalone application

a-f. Visualization of a 64-cell stage Phallusia mammillata embryo with labeled cell nuclei and cell membranes. a-c intensity images showing the nuclei (a), the membranes (b) or both (c). d. same as c. with additional nuclei segmentation obtained with the Binarize plugin (see Supp. Mat. for the full description of curation plugins). e. same as b. With additional membrane segmentation obtained with the Cellpose 3D plugin. f. same as c. with a combination of several rendering possibilities of cell and nuclei segmentations.

g. Multi-colored shaders allow the simultaneous visualization of the expression patterns of multiple genes extracted from the ANISEED17 database and of tissue fate information. Ascidian embryo16 at stage 15 (mid neurula); cells with a single color are coloured with larval tissue fate; multi-coloured cells are coloured with both larval tissue fate and the expression of selected genes.

h. Visualization of a 6 days post-fertilization Platynereis dumerilii embryo20 imaged by whole-body serial block face scanning electron microscopy followed by the automated whole-cell segmentation of 16000 cells.

i-k. Visualization of a cell cycle 14 Drosophila melanogaster embryo imaged with SiMView microscopy and segmented with RACE21. i. Projection on each segmented cell of the mean image intensity. j. Projection on each segmented cell of the ratio between the length of the major and the minor axes of the ellipse that has the same normalized second central moments as the segmented cell. k. projection of the cell volume.

MorphoNet Standalone Schema:

From the local data (loaded from the green box), the MorphoNet Standalone application computes first the dual meshes for each of the segmented objects (in the module python in the yellow box). Then, using the 3D viewer (in the blue box), users identify detection, segmentation or tracking issues using, if necessary, the cell lineage information, the raw images and/or properties computed on the segmented objects. Errors are then corrected by choosing and executing the appropriate image processing plugin from the curation menu. Finally, new meshes are computed from the result of the plugin execution to update the visualization.

Unsupervised quality assessment and curation of the Tribolium castaneum embryo

a. The 5 steps of the curation pipeline.

b. View of the original intensity images (in green) of the first time step of the published data6. Both Ground Truth channel (GT, red point) and Silver Truth (ST, white nucleus segmentation) are shown at the top. Blue segmentation corresponds to the match between ST and GT. Bottom, zoom at the GT region (ROI) without the intensity images.

c. Projection for the ST of the distance between the gravity center of the intensity inside the segmentation and the centroid of the segmentation. Color bar at the bottom of d.

d. Same as c. for the curated pipeline.

e. Projection for the ST of the deviation of the intensity at the border of the segmentation. Color bar at the bottom of f.

f. Same as e. for the curated pipeline.

g. Comparative histogram of the intensity_offset property distribution between the ST, the Step 1 and the Step 5 for the 181 curated nuclei (left) and the whole image (right).

h. Same as g for the distribution of the intensity_border_variation property.

i. Sams as g. For the distribution of the nuclei volume property.

Starfish whole-cell segmentation using Cellpose

a. Animal and Lateral view of the maximum intensity projection from the published dataset23.

b. Segmented ground truth image.

c. Result of the segmentation using Cellpose Cyto2 model followed by the removal of small cells (<1000 voxels) with the Deli plugin

d. Result of a Cellpose segmentation with a model trained on P. miniata dataset followed by the Deli plugin.

e. New cells created (different between b and d)

f. Under segmentation and missing cells generated by d. compared to b.

g. Vegetal view of c with smoothness representation.

h. opposite view of d with smoothness representation.

i. Cell size distribution in the published segmentation (b), Cellpose cyto2 model (c) and Cellpose with P. miniata model (d).

j. Identical as i after application of the Deli plugin.

Colors in b-f, represent cell volume in µm3.

Colors in g,h represent Smoothness.

Curation of a segmented shoot apical meristem of Arabidopsis thaliana.

Visualization of the time step n°19 for several types of curation using MorphoNet.

a. 3D view of an Arabidopsis thaliana shoot apical meristem25.

b. Published 3D intensity images.

c. Published 3D segmentation of an Arabidopsis thaliana shoot apical meristem25 obtained using MARS-ALT26.

d. Comparative histogram based on the cell volume between the published segmentation (c), the result of the cyto2 prediction (e) and the final curated version (i) + Deli plugin for cells <1000 voxels. X and Y axes are in log scale.

e. Result of the Cellpose28 3D MorphoNet plugin using the pretrained cyto2 model.

f. Result using the Cellpose 3D MorphoNet plugin using the model trained over the 10 first time steps with the Cellpose training plugin with the XY planes.

g. Result of the Cellpose 3D MorphoNet plugin using the model trained over the 10 first time steps with the Cellpose training plugin with each plane of the 3D images.

h. Manually selected masks using morphonet on published data (c).

i. Result of the Cellpose 3D MorphoNet on the selected masks (h) using the model trained over the 10 first time steps with the Cellpose training plugin with each plane of the 3D images.

Curation of a Caenorhabditis elegans embryo dataset

a. Cell lineage viewer of all time steps colored by clonal cells of the published segmented dataset29.

b. Comparative histogram based on the axis ratio between the published data and the curation.

c. 3D View of the intensity images at t=150.

d. 3D View of the published segmented dataset at t=150. Colors represent the ratio of the longest axis on the shortest axis of the shape.

e. Automatic selection (in gray) of the nuclei with an axis ratio>2.9.

f. Result of the Fusoc plugin applied on all selected nuclei. Colors represent the nuclei volume in µm3.

g. Same as f. But only previously selected nuclei are shown.

h. Result of the Gaumi plugin applied independently on regions fused with 4,3 or 2 nuclei. Colors represent the axis ratio as in d.

Curation of a Phallusia mammillata ascidian embryo named Astec-Pm9 in the publication16.

a. Cell lineage of the cell b7.1 after the execution of the Disco and Deli plugins on the published data. Projection of the volume property, the colormap between b and c represents the cell volume in µm3.

b. Scatter view of the corresponding segmented embryo described in a. at t=28 colored by cell volume. Colormap identical as a.

c. Same view as c. with the activation of the “highlight” mode which focuses on the selected cell and shows other cells in transparents colors.

d. Several snapshots of the cell b8.21 at different time points with its associated cell lineage. Colormap represents the cell volume in µm3 which points to a missing division.

e. Cell lineage of the bilateral cells b7.11 and b7.11*. Colorbar shows the lineage distance between the bilateral symmetrical cells. Black region represents snapshots with no matches between bilateral symmetrical cells.

f. Cell lineage of the bilateral cells a7.5 and b8.6. Colorbar shows the compactness property. The property highlight that the delay of division between A7.5* and A7.5 is due a under-segmented error of A7.5*. B8.6 and B8.6* have expected behavior.

g. Result of the Fuse plugin applied on an over-segmented cell.

h. Top line: Several snapshots of B7.7* cell under-segmented (between time point 31 and 33) from the original segmented embryo. Bottom: result of the Propi plugin applied backward from time t=34 where both cells are well separated.

i. Example of the result of the Wata plugin from a manual added seed (red dot) in the empty space.

j. Result of the Copy-Paste plugin from the selected cell (in gray) on the left side of the embryo to the right side (the new cell appears with a mesh shader in blue). Colormap represents cell volume in µm3.

k. Comparison of the lifetime of bilateral symmetrical cells. The X axis shows the number of in time points separating the division of bilateral cell pairs. The Y axis corresponds to the number of cell (in log)