Given a set of spatially co-colocalized points that share the same factor annotation, allow users to highlight these points by generating a convex hull around them. This will be useful, for example, for cases where each point is an mRNA in space annotated based on which cell they are assigned to. We can then make a convex hull around the mRNAs belonging to each cell to get a sense of the cell segmentation. This is also useful for cases where each point is a cell on a tSNE annotated based on cell type, etc. Other minimum bounding box algorithms may also be considered.

Potential libraries:

• https://github.com/AndriiHeonia/hull (appears to only handle 2D cases though)
  
• https://threejs.org/docs/#examples/quickhull/QuickHull
• https://github.com/mauriciopoppe/quickhull3d (https://codesandbox.io/s/mQ7AgN1n)

Implementation in deck.gl:

• Use a polygon layer (https://github.com/uber/deck.gl/blob/master/docs/layers/polygon-layer.md) or geojson layer (https://www.youtube.com/watch?v=OR561rc5VG0)

Alternatively, a geojson file can be provided. However, if it's not provided, more time will be spent to generate it from the csv data.

Hi, thank you for making the tool. I was following the step of Run without re-building. However, the website http://localhost:8080/ doesn't load. Could you tell me if I did anything wrong?

Minimum viable product aim: Given a bg.tif image in the same folder as index.html, create a bitmap layer as the background.

Hello, I was trying to replace the bg.png with my own data and found out it lost the original ratio and became 1:1 (width:length). Is it possible that the ratio can be maintained after uploading? Sorry, my JAVASCRIPT knowledge is very limited. But I guess that we will change around IMAGES.BG. Thank you so much for spending time to look into it.

Enhancements

• Provide option to disable rotation
• Loading bar
• Generalized gene.csv to be matrix of options where reach column may be a different category to visualize gene.csv no longer used
• Generalize data.csv to accommodate any number of metadata columns (including each point being a cell and metadata being numeric gene expression)
• Allow for numeric / non-categorical color scales
• Allow user to select colors
• Enable uploading own data
• Reset to center option
• Prevent zooming too far away Sufficient with reset

Known bugs

• Resetting gene does not automatically change point size, only color
• Reset view triggers with new gene selection?

• CZI cellxgene: https://github.com/chanzuckerberg/cellxgene - React + Redux app for exploration of large scale scRNA-seq datasets
• Google Neuroglancer: https://github.com/google/neuroglancer - WebGL-based viewer for volumetric data
• Sten Linnarson's mouse brain explorer: http://loom.linnarssonlab.org/dataset/cells/osmFISH/osmFISH_SScortex_mouse_all_cells.loom/NrBEoXQGhYDYoAZrAMxQIwvQJm1VfAFnwFZ858B2CFYDAlBvGB5VzJqEu~gzJAOaJMiEcCqD2wABxTaHdGyFQcIjGJgBOeaxH6FfIvsENjq9Zom7Z8ruZMNUOtaPE6Deu9DOHwdAFpEADpEVDgiLS1EHFQiVCpSJGD4uAjSUkQqGQwccn4iVVMWYHE~aQYsDhKnQxATADsAVwAbFtNBVw1xE2lehX7TQ3RmtsF6HFUkuSTUBgQcSckcOQxl3EkMBErcQow5HAXhbkwknB0XTB0MQtR1J0mNRiGIIA

Hi: Do you think it would be ok to use the data you have here as another demo in Vitessce, which I'm working on for Peter? I see the link for the molecules csv, but is there a good way to get the background bitmap or the cell outlines?

hellow, I met HTTP 404 error when replacing the data.csv.gz file in the build/ folder and follow the Run without re-building steps. And the the page could not be loaded.

If I do not relace the file, I will not encounter this problem

Serving HTTP on 0.0.0.0 port 8080 (http://0.0.0.0:8080/) ...
"GET / HTTP/1.1" 200 -
code 404, message File not found
"GET /MERmaid/static/js/main.92048d1f.js HTTP/1.1" 404 -
code 404, message File not found
"GET /MERmaid/manifest.json HTTP/1.1" 404 -

Hi, I used STARFISH, a program that analyzes transcriptome imaging, to produce a data.csv.gz file for visualization with MERmaid. However, there are 3 TypeErrors associated with the same object, called this.props.color, which seems to be Null/undefined. I believe this may be an issue with STARFISH, as the way they write the file might be out of date. A link to the data.csv.gz file is below. Can you please give me some insight on whether the file is out of date or if it is an issue with MERmaid? Thank you.
https://drive.google.com/file/d/1Uzq9U5iKa466E8FPrJEwq_2wV3AnaMCu/view?usp=sharing

To be clear, I rebuilt using "npm install" and then opened this tab using "npm start". When I tried running without re-building, I simply got the error message "code 404, message File not found", which seems to be a separate issue.