The eLogbook is the central hub for data management and data processing. It is a website at https://cryoem-logbook.slac.stanford.edu. It will (amongst other things) will:
- Provides an interface for operators to manage experiments
- Automatically move the data from the microscopes to the clusters
- Setup permissions on the data
- Setup remote access so that users may control the TEMs via FastX
- Provide image and data previews of aligned, ctf'd and picks images in near real time via SLACK
- Provide summary information of the experiment (histograms of resolution etc)
- Provide 'notebook' functionality to allow users to annotate and log their experiment
As an Operator
The role of an operator is to prepare the data management and pre-processing pipelines for a microscope user. This entails:
- Creating an 'experiment' in the following nomlecture: YYYYMMDD-<PROPOSAL ID>
- One can clone an existing experiment (recommended) or create a new one
- Edit the experiment (in the list of experiments) with the appropriate details: specifically include
- The name and email of the PI
- add a 'Leader' to the experiment (SLAC unix username) - this person should be the person who is physically running the experiment and collecting data
- Assign the correct TEM to the experiment
- Once an experiment has been prepared, it can must be 'switched' on with the appropriate TEM.
- Once an experiment is finished, the TEM should be put into standby
...
- the type of data collection you are performing [
tomography
orsingle-particle ]
the image format you are collecting with [
.tif
or.mrc
]- the apix value
- the fmdose (A^2 per frame) - used for motioncor2
- whether the images are
superres
(set to1
for yes,0
for no) - whether the images are collected using a
phase_plate
or not.
...