Wiki Page Content

Metadata Stored in JSON files

JSON files in the info folder

JSON files are human-readable and editable text files, which are also software-friendly. This is rapidly becoming one of the most common formats used in the web-development community. They have a '.json' extension, and can be opened in any text-editor.

For more information on these files and accessing them in EMAN2, see Eman2JSStorage.

While these files are human-readable, using the "Info" button in the EMAN2 file browser will give a much more convenient way to look at the contents of these files.

If you have a micrograph called, for example, micrographs/DC19873.hdf, and have processed it with EMAN2, you will end up with other derived image files, such as particles/DC19873_ptcls.hdf and particles/DC19873ctf_flip.hdf, etc. Any information which needs to be stored about the micrograph as a whole, will be stored in info/DC19873_info.json. If you wish to copy micrographs from one project to another, all you need to do is copy the image file(s) and this JSON file to the info/ folder in the new project.

project.json

This file contains overall project parameters, such as A/pix, voltage, mass, etc.

Parameter

Description

global.apix

A/pixel value for this project. Generally speaking, if you want to downsample/rescale your data, you should do this in a separate project.

global.microscope_voltage

Default microscope voltage in kV when running CTF fitting and micrograph evaluation programs. While it is technically possible to combine data from multiple micrographs in a single project, it is not usually a good idea. If you are thinking about doing this you may wish to ask us about it first.

global.microscope_cs

Default Cs value in mm when running CTF fitting and micrograph evaluation programs.

global.particle_mass

The default mass of the particle being reconstructed in kDa. Clearly in some cases (assemblies in various stages of assembly, etc.) there will not be a single value for this. This value is primarily used as a default, and is really only used for setting reasonable isosurfaces in any case, so such situations should not really be a problem

global.boxsize

The default box-size used by e2boxer and other programs. Specified in pixels in the fully sampled micrographs.

global.ptclsize

Estimated maximum dimension of the particle being reconstructed measured in fully sampled pixels.

global.invariant_type

Which type of invariants this project uses. Changing invariants requires redoing particle preprocessing, so it is considered a property of the project. "bispec" or "harmonic" are the current choices.

project_icon

Used by the GUI

project_name

For recordkeeping purposes

notebook.json

This is where the projectmanager stores the text entered in the 'lab notebook'.

<micrograph>_info.json

Per micorgraph information is stored in one file for each micrograph. This allows easy copying of micrographs with their metadata between projects. While there is, of course, metadata in the image headers, THIS metadata is not stored in the header because the information, such as CTF information, is associated with multiple image files, including the micrograph itself, as well as particle stacks, etc.

Parameter

Description

boxes

list of lists. Each item in the list is a 3 element list containing (X-center,Y-center,method), where type is a string describing the method used to find the particle, eg- "manual",...

boxes_3d

list of lists. Each item in the list is a 4 element list containing (X-center,Y-center,Z-center,method,[score,[class #]]), where method is a string describing the method used to find the particle, eg- "manual",..., class # is an integer grouping similar particles, score is an arbitrary float (lower better)

boxes_rct

list of lists. Each item in the list is the same as in "boxes" above. type is "tilted" or "untilted"

ctf

A list of CTF related objects: [EMAN2CTF instance,signal 1D,background 1D] computed from particles, not the overall frame. Note, prior to 5/18/16 im_2d and bg_2d were also stored here

ctf_im2d

2d power spectrum average of particles from this image

ctf_bg2d

2d background power spectrum from particles in this image

ctf_frame

A list of CTF related objects associated with the whole frame: [box size,EMAN2CTF instance,box coord,set of excluded boxnums],quality (old location),oversampling

ctf_microbox

A 1-D power spectrum computed from the whole micrograph with the same box size and mask as individual particles. Only generated if e2ctf.py has the correct options

quality

A single integer from 0-9. No predefined meaning, though 5 is the default value, and larger should be interpreted as better. This is to permit qualitative assessement by the user at various stages of analysis.

sets

A dicitionary containing lists of integers keyed by set name

bad_particles - Particle numbers which have been determined to be 'bad'. The 'bad' particles may optionally be excluded when building sets

Eman2InfoMetadata (last edited 2019-03-23 16:50:41 by SteveLudtke)