FIB-SEM datasets of the Anaeramoeba flamelloides BUSSELTON2 symbiosome
type: Dataset
distribution: Landing page for the dataset
description: FIB-SEM Cells were grown on Sapphire discs and high-pressure frozen in 100 µm deep golden carriers in an HPM100 (Leica microsystems, Wetzlar, Germany) with 20% BSA in ASW as cryo-protectant. The cells Freeze substitution was performed as in Guo et al¹⁰, but with shorter washing steps for the sake of time. After freeze substitution, the samples were infiltrated with TAAB embedding resin hard grade (TAAB Laboratories, Aldermaston, England). The sample was mounted on an SEM-stub with epoxy and silver glue. The sample was further coated with 5nm Pt to reduce charging. Volumes were acquired using a Scios dualbeam (FEI, Eindhoven, The Netherlands) with the electron beam operating at 2 kV/0.2 nA, detected with the T1 In-lens detector. To automate the acquisition, we use the Auto Slice and View 4 software provided with the microscope. A 700 nm protective layer of platinum was deposited on the selected area before milling. The volume was further registered and processed by the ImageJ plugins Linear alignment by SIFT and Multistackreg. After registration, the volumes were converted to mrc-files, and the header was modified to recover the pixel size that got lost during conversion. The resolution of the two volumes and the number of slices were: 9235_1 (8.43 nm x 8.43 nm x 8.0 nm), 1,725 slices, and 9235_2 (6.744 nm x 6.744 nm x 7.0 nm), 1,300 slices. Segmentation The A. flamelloides BUSS2 cells were segmented by a combination of manual segmentation and Deep Learning Segmentation in Microscopy Image Browser v2.91 beta 45¹¹,¹². Training sets were assembled using the Segment Anything Model 2 (SAM 2). The training dataset for endoplasmatic reticulum and endocytic compartments was assembled by using the whole model and gradually using the different individual models to cut out the model. The final cut out introduced to the mask and used for mask-restricted BW thresholding to yield the respective training slices. Briefly, Desulfobacter sp. symbionts, whole cells, symbiosome, endopl…
modified: 2026-04-14T00:00:00Z
issued: 2026-04-14T00:00:00Z
publisher: Uppsala University
theme: HEAL
qualified attribution: Attribution
  had role: principalInvestigator
  agent: Jon Jerlström-Hultqvist
    type: Agent
    account: https://orcid.org/0000-0002-7992-7970
    type: PrivateIndividual(s)
keyword: Evolutionary biology not elsewhere classified
keyword: Cellular interactions (incl. adhesion, matrix, cell wall)
keyword: Microbiology not elsewhere classified

Landing page for the dataset
type: Distribution
title: Landningssida för datasetet @sv
access URL: FIB-SEM datasets of the Anaeramoeba flamelloides BUSSELTON2 symbiosome
availability: stable

Uppsala University
type: Agent
name: Uppsala universitet @sv
type: Academia-ScientificOrganisation
source: https://ror.org/048a87296