Back

OpenFIBSEM: an application programming interface for easy FIB/SEM automation

Cleeve, P.; Dierickx, D.; Buckley, G.; Gorelick, S.; Naegele, L.; Burne, L.; Whisstock, J. C.; de Marco, A.

2022-11-02 cell biology
10.1101/2022.11.01.514681 bioRxiv
Show abstract

Automation in microscopy is the key to success in long and complex experiments. Most microscopy manufacturers provide Application Programming Interfaces (API) to enable communication between a user-defined program and the hardware. Although APIs effectively allow the development of complex routines involving hardware control, the developers need to build the applications from basic commands. Here we present a Software Development Kit (SDK) for easy control of Focussed Ion Beam Scanning Electron Microscopes (FIB/SEM) microscopes. The SDK, which we named OpenFIBSEM consists of a suite of building blocks for easy control that simplify the development of complex automated workflows.

Matching journals

The top 4 journals account for 50% of the predicted probability mass.

1
PLOS ONE
● 4510 papers in training set
Top 8%
19.1%
2
Journal of Microscopy
○ 18 papers in training set
Top 0.1%
17.9%
3
Journal of Structural Biology
○ 58 papers in training set
Top 0.1%
10.7%
4
Scientific Reports
○ 3102 papers in training set
Top 30%
4.1%
50% of probability mass above
5
HardwareX
○ 16 papers in training set
Top 0.1%
3.1%
6
Communications Biology
○ 886 papers in training set
Top 4%
2.4%
7
Wellcome Open Research
○ 57 papers in training set
Top 0.6%
1.9%
8
eLife
● 5422 papers in training set
Top 37%
1.9%
9
Nature Communications
○ 4913 papers in training set
Top 49%
1.8%
10
Nature Methods
○ 336 papers in training set
Top 4%
1.7%
11
Journal of Structural Biology: X
○ 15 papers in training set
Top 0.1%
1.7%
12
Microscopy and Microanalysis
◐ 12 papers in training set
Top 0.1%
1.5%
13
Frontiers in Cell and Developmental Biology
○ 218 papers in training set
Top 5%
1.5%
14
SoftwareX
○ 15 papers in training set
Top 0.2%
1.4%
15
Journal of Cell Biology
● 333 papers in training set
Top 3%
1.4%
16
Data in Brief
○ 13 papers in training set
Top 0.1%
1.4%
17
iScience
○ 1063 papers in training set
Top 21%
1.3%
18
BMC Methods
○ 11 papers in training set
Top 0.1%
1.0%
19
Laboratory Investigation
○ 13 papers in training set
Top 0.1%
1.0%
20
Optica
● 25 papers in training set
Top 0.6%
0.9%
21
Cell Reports Methods
○ 141 papers in training set
Top 4%
0.9%
22
Viruses
○ 318 papers in training set
Top 5%
0.8%
23
Journal of Visualized Experiments
● 30 papers in training set
Top 0.7%
0.8%
24
Optics Express
● 23 papers in training set
Top 0.5%
0.7%
25
ACS Nano
● 99 papers in training set
Top 4%
0.7%
26
EMBO Reports
○ 88 papers in training set
Top 0.9%
0.7%
27
IUCrJ
● 29 papers in training set
Top 0.4%
0.7%
28
Biophysical Journal
○ 545 papers in training set
Top 6%
0.5%
29
Open Research Europe
○ 14 papers in training set
Top 0.3%
0.5%
30
Biology Open
● 130 papers in training set
Top 4%
0.5%