The SerialEM Script Repository

Seri­alEM is a soft­ware devel­oped at the The Boul­der Lab­o­ra­tory for 3D Elec­tron Microscopy enabling acqui­si­tion of a vari­ety of data from trans­mis­sion elec­tron micro­scopes: tilt series for elec­tron tomog­ra­phy, large image areas for 3D recon­struc­tion from ser­ial sec­tions, and images for recon­struc­tion of macro­mol­e­cules by single-particle meth­ods.

Seri­alEM also fea­tures a pow­er­ful script­ing lan­guage (until ver­sion 3.6.0 in 2016/17: “macros”) allow­ing to con­trol var­i­ous micro­scope para­me­ters, acquire, process and save images, and call higher level func­tions of Seri­alEM such as aut­o­fo­cus, walk-up, align­ment to ref­er­ence images, or auto­matic adjust­ment of inten­sity. For tasks of higher com­plex­ity, Seri­alEM scripts can include con­trol struc­tures such as con­di­tional expres­sions, loops, and func­tions.

Nex­pe­rion has set up a pub­lic repos­i­tory for Seri­alEM scripts (macros) in col­lab­o­ra­tion with the devel­oper of Seri­alEM to serve as a cen­tral shar­ing point for scripts, to make them eas­ily acces­si­ble in a well organ­ised and doc­u­mented way, and to stim­u­late exchange between Seri­alEM users. To access the scripts avail­able via the repos­i­tory, start­ing at a cat­e­gorised list, no reg­is­tra­tion is required. To upload new scripts or to edit their own exist­ing scripts, users need to reg­is­ter.

This site uses cook­ies, to help pro­vide you with the best user expe­ri­ence we can. By con­tin­u­ing to browse the site, you are agree­ing to our use of cook­ies as out­lined in the pri­vacy pol­icy.