Evidence map›Paper›PMID 31994199›Full record

ArticleJournal of microscopy2020

Quantitative method for estimating stain density in electron microscopy of conventionally prepared biological specimens.

A Fera, Q He, G Zhang, R D Leapman

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of microscopy, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed.

  1. Which resolution?IUCrJ · 2023
    Article
  2. Article
  3. Upscaling X-ray nanoimaging to macroscopic specimens.Journal of applied crystallography · 2021
    Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

4 authors.

A FeraNational Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, U.S.A.
Q HeNational Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, U.S.A.
G ZhangNational Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, U.S.A.
R D LeapmanNational Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, U.S.A.ORCID 0000-0002-8575-4084

Funding

Scanning Transmission Electron Tomography of Biological StructuresZIAEB000046 · NIBIB · NATIONAL INSTITUTE OF BIOMEDICAL IMAGING AND BIOENGINEERING · PI LEAPMAN, RICHARD · 2009 to 2025
$13.0M
Electron Tomography Of Cellular StructuresZ01EB000017 · NIBIB · NATIONAL INSTITUTE OF BIOMEDICAL IMAGING AND BIOENGINEERING · PI LEAPMAN, RICHARD · 2007 to 2008
$56k
Intramural NIH HHS Z01 EB000017
6 · The paper itself

Abstract

Stain density is an important parameter for optimising the quality of ultrastructural data obtained from several types of 3D electron microscopy techniques, including serial block-face electron microscopy (SBEM), and focused ion beam scanning electron microscopy (FIB-SEM). Here, we show how some straightforward measurements in the TEM can be used to determine the stain density based on a simple expression that we derive. Numbers of stain atoms per unit volume are determined from the measured ratio of the bright-field intensities from regions of the specimen that contain both pure embedding material and the embedded biological structures of interest. The determination only requires knowledge of the section thickness, which can either be estimated from the microtome setting, or from low-dose electron tomography, and the elastic scattering cross section for the heavy atoms used to stain the specimen. The method is tested on specimens of embedded blood platelets, brain tissue and liver tissue.

Indexed as

Microscopy, Electron, TransmissionAnimalsBlood PlateletsBrainBrain ChemistryColoring AgentsHistocytological Preparation TechniquesHumansLiverMiceMicrotomyStaining and LabelingColoring AgentsElastic scattering cross sectionsplastic embedded blocksserial block-face electron microscopystain densitytransmission electron microscopy

Identifiers

PMID31994199
PMCPMC7530943

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.