Featured Useful resource: MorphoNet – the Node

Doing nice science is dependent upon teamwork, whether or not that is throughout the lab or in collaboration with different labs. Nevertheless, generally the assets that assist our work might be missed. Our ‘Featured useful resource’ collection goals to shine a light-weight on these unsung heroes of the science world. In our newest article, we hear from Patrick Lemaire and Emmanuel Faure, who describes the work of MorphoNet.

Patrick Lemaire¹ and Emmanuel Faure ²

1. CRBM, Université de Montpellier, CNRS, 34293 Montpellier, France.
2. LIRMM, Université de Montpellier, CNRS, 34095 Montpellier, France

What’s MorphoNet?

MorphoNet (1) is an interactive morphodynamic net browser designed to assist scientists, lecturers and college students share, analyze and visualize the big 3D morphological datasets that may be generated by fashionable imaging know-how, starting from dwell gentle sheet microscopy of cells and embryos to X Ray tomography of fossils.

Why did you construct MorphoNet?

We initially created MorphoNet in order that our biologist collaborators can work together, with out programming abilities, with the 3D + time datasets they obtained by gentle sheet microscopy of dwell ascidian embryos adopted by segmentation (2). We wished the system to be web-based in order that they don’t have to put in any subtle software program on their computer systems, and to permit knowledge sharing. We due to this fact selected to make use of a highly regarded gaming engine Unity, to point out meshed segmented knowledge. This alternative allowed us to compress the advanced 3D + time datasets sufficiently in order that they may very well be explored, curated and shared by means of an intuitive graphical person interface, operating on a normal net browser. In an identical method as genomic browsers show genetic options and epigenetic or gene expression knowledge as traces onto the first genome sequence, quantitative and qualitative data might be imported and projected onto particular person or grouped segmented objects in MorphoNet. These ‘morphological augmentations’ might be saved and shared with different customers (and utilized in publications), respecting the FAIR philosophy.

Can I exploit the system with my knowledge?

In fact! It’s open-source, publicly obtainable and we commit to not make any scientific use of your personal knowledge! After a free registration to the service, you possibly can add as much as 10Gb of information. This area is enough for 20 motion pictures just like the one proven in Determine 1 – prime left. Should you want extra storage, please contact us, we are going to discover a resolution. There are two methods of importing your individual knowledge to MorphoNet: remoted time factors might be uploaded with a devoted Fiji plugin: https://morphonet.org/help_fiji.

Extra advanced datasets (e.g. time collection) might be uploaded by means of the python API: https://morphonet.org/help_api

What kind of information can I add and visualize?

Though customers can add and visualize uncooked depth photos, MorphoNet’s full potential is unleashed when working with 3D (+ time) segmented knowledge. When you have not but generated meshes to your segmentations, the system will routinely carry out this activity for you.

MorphoNet really provides extra flexibility than genome browsers. Whereas the DNA base pair is the common unit of data in genome browsers, the selection of the related morphological unit of data (i.e., the dimensions of the segmented objects) in MorphoNet is left to the person, from complete organs right down to molecular complexes (Determine 1). Like all web-based system MorphoNet has some limitations, that are progressively lifted because the webGL know-how is progressing. It’s presently tough to visualise tissues of embryos with greater than a few thousand segmented cells or objects.

Can I see contained in the imaged object?

Uploaded datasets are totally interactive. You possibly can rotate, zoom in or out, and click on on every particular person object. To discover the within of your segmented buildings, you possibly can simply take away whole cell layers, or individually choose and conceal particular person objects. You may as well use the scatter view to actually explode all objects radially to obviously visualize every of them (See under).

Can I concurrently visualise several types of segmented objects (e.g., nuclei inside complete cells)?

Sure. You possibly can add datasets with a number of segmented channels, obtained from membrane and nuclei recordings, for instance. You may as well instantly add your uncooked depth photos to your scene. This may be very helpful to see gene expression over cell segmentation for instance.

Can I annotate my dataset with MorphoNet?

Sure. MorphoNet can be utilized so as to add several types of annotations to your dataset: temporal (i.e. to hyperlink objects by means of time), qualitative (for instance, to call objects), quantitative (to attribute a price to every particular person component, for instance cell quantity (see under)), a range worth (a given quantity for every objects) and others (particulars of the codecs used might be discovered right here https://morphonet.org/help_format ). You possibly can both instantly label your objects within the scene or add an annotation file.

Can I assess the standard of my segmentation with the unique microscope photos?

Sure, you possibly can add the unique microscope photos used to phase your dataset and evaluate them together with your segmented knowledge. You possibly can both show the complete 3D quantity utilizing a threshold worth to take away the background or simply present some slices in X, Y or Z. You possibly can take a look at this instance.

Can I exploit MorphoNet to visualise Gene Expression Information?

Sure, for ascidian embryos, MorphoNet is interfaced to the gene expression part of the ANISEED database (https://www.aniseed.cnrs.fr) (See Determine 2 and film under).  Different exterior gene expression databases may very well be linked to MorphoNet sooner or later, and we shall be blissful to work with you on such initiatives. If no gene expression database is obtainable to your organism, you possibly can instantly add your expression profiles utilizing a easy format (https://morphonet.org/help_format) after which, as we did with the Arabidopsis meristem (3), you possibly can manually curate, if mandatory, your gene expression data by labeling particular person cells.

To discover gene expression knowledge, every particular person gene might be assigned a color, and the highly effective MorphoNet shaders can help you concurrently visualize the expression profiles of as much as 4 genes. You may as well interrogate your knowledge for genes expressed within the intersection or the union of some particular chosen cells.

Can I discover the cell lineage?

MorphoNet is a singular device which lets you work together on the similar time together with your 3D+t dataset and the corresponding lineage. We use a second window to show the cell lineage and every click on on a selected cell may also be displayed on the lineage. You may as well map supplementary data, such because the cell quantity, on the lineage  after which order the branches by these values.

How can I make good figures from MorphoNet?

We lately applied a brand new module (contained in the instruments menu), which lets you create your individual figures in pdf format. You may as well create your individual motion pictures in MorphoNet. Merely outline some key frames and MorphoNet will interpolate the remaining.

How can I share knowledge with my colleagues?

You possibly can simply share a selected dataset you personal with any colleague who registered to MorphoNet. If you wish to share a number of datasets, you possibly can group them right into a working group, which might be shared.  You may as well use MorphoNet to share knowledge publicly, in an article for example. For this, you possibly can create a session, with a everlasting url that may be shared (Simply click on right here for instance https://morphonet.org/hgCbNDIV).

Can I do extra if I can code? 

You possibly can instantly question your knowledge utilizing the python API : https://morphonet.org/help_api. It is extremely helpful when you may have many datasets or whenever you routinely compute some properties.  We’re additionally creating a Plot module which permits us to instantly visualize your knowledge inside our 3D viewer with none knowledge add.  And you’ll, after all, contribute! MorphoNet is an open-source software program. Please contact us in case you are . We’re having a number of enjoyable.

What are the following options that you just plan so as to add in MorphoNet?

We’ve got a number of initiatives underway. We’re presently engaged on a standalone utility which you’ll instantly set up in your pc to completely exploit its computational assets when interacting with huge datasets.

We’re additionally engaged on the Digital Actuality illustration of your knowledge. It will can help you work together with your individual knowledge with a classical VR headset.

Keep tuned!  You possibly can observe us on Twitter @MorphoTweet

REFERENCES:

1. B. Leggio, J. Laussu, A. Carlier, C. Godin, P. Lemaire, E. Faure, MorphoNet : an interactive on-line morphological browser to discover advanced multi-scale knowledge. Nat Commun. 10, 1–8 (2019).
2. L. Guignard, U.-M. Fiúza, B. Leggio, J. Laussu, E. Faure, G. Michelin, Ok. Biasuz, L. Hufnagel, G. Malandain, C. Godin, P. Lemaire, Contact space–dependent cell communication and the morphological invariance of ascidian embryogenesis. Science. 369, aar5663 (2020).
3. Refahi et al.    A multiscale evaluation of early flower growth in Arabidopsis offers an built-in view of molecular regulation and progress management. Developmental Cell, Elsevier, 2021, 56 (4), pp.540-556.e8. ⟨10.1016/j.devcel.2021.01.019⟩

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