yilaili / cryoem-viztools Goto Github PK

Input: *.star (info at the microgarph level)
Output: *.png (one png for each micrograph listed in star file)

Display:

• micrograph image
• attributes in star file displayed next to the micrograph image

else skip

Add a flag to enable making multiple scatter plots or histograms in starviz.py as frames.

Input: *.star (info at the particle level)
Output: *.html

Features:

• Can select different data frames in the dictionary read in (data_optics and data_micrographs).
• Show histograms with a slider to filter different attributes (selectable). Also show the total number after filtering.
• 2D scatter plot with any two selected attributes.
• Enhancement: can select each micrograph entries and view where it comes from on the micrograph as images along with the associated attributes. We will have a separate flag to enable this.

Input: *.mrc
Output: *.html
Features: zoom-in/out, translation, rotation, filtering based on voxel values

to mrc2png.py, eps2png.py and overlay.py. Will skip the file already converted.

Input: *.mrc and *.star (coord)
Output: *.html

Features:

• The images will be displayed in a selectable list.
• The coordinates encode the positions of certain points on a certain image. We'll need to overlay the coordinates on top of the images as circles.
• Have a sliding bar to display coordinates only above a certain threshold. (Optional)
• Change the diameter of the circles.
• Change the color of the circles.

Select a subset of star file based on one attribute and given range or indices.
Output a new star file.

For python (conda env) and also node modules.

Could use os.walk.

Only input would be RELION's AutoPick job folder. Will look for summary.star for paths of both micrographs and picks.

Output will be a tiled image.

Input: *.star (info at the particle level)
Output: *.html (one html for each micrograph listed in star file)

Display:

• scatter plot of rlnCoordinateX and rlnCoordinateY overlaid on micrograph image, with selectable color coding
• one html for each unique micrograph in the star file

see: https://stackoverflow.com/questions/71051126/how-to-plot-a-heat-map-on-spherical-surface-having-azimuth-and-elevation-and-a-c

Azimuth and elevation will be read from particles.star file (should be rot and tilt).

Title is the input mrc name.

Project a 3d mrc file along x y z axis and tile the images.

As title.

Input: *.star (info at the micrograph level)
Output: *.html

Features:

• Can select different data frames in the dictionary read in (data_optics and data_micrographs).
• Show histograms with a slider to filter different attributes (selectable). Also show the total number after filtering.
• 2D scatter plot with any two selected attributes.
• Enhancement: can select each micrograph entries and view each of them as images along with the associated attributes. We will have a separate flag to enable this.

Input: *.pdb
Output: *.html
Features: zoom-in/out, translation, rotation.