Microscope Slide digitisation 2D+ (RBINS/RMCA )

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Equipment

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Staff training

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Description

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Size of the objects

Illustrated description

The system from 'Information in Images' is mounted onto an existing microscope system (https://www.informationinimages.com/auto-scan-micro).

It allows to make a gigapan composite image of a slide at the available magnifications (10x, 20x, 40x, 100x) and includes Z-Stacking.

The (composed) images per Z-Level can be processed through the manufacturer's stacking software or using Zerene Stacker software (https://zerenesystems.com/cms/stacker) or Helicon Focus (https://www.heliconsoft.com/heliconsoft-products/helicon-focus/).

Results

Picture of a copepod composed of several stitched tiles of stacked pictures at high magnification.

https://europeanjournaloftaxonomy.eu/index.php/ejt/article/view/895

Contributors: Picture: A. Mathys

Copyright: RBINS / AGORA-3D Belspo Licence: CC BY NC ND

Click on the image to see the full resolution image

Use-cases

References

Pipeline

Digitisation procedure

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Open Source softwares

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Standardisation protocols

Semantics

Storage capabilities

Data access

Data/image analysis

Cost(s)

Human Time Generating and processing datasets - Requirements in human time

-Preparation time: Cleaning the slides (dust removal and possible fingerprints) and placing the slide on the slide table takes only a minute or two. -Digitization procedure: The specimen has to be located and a specific magnification has to be chosen. Next, the amount of Z-stacking has to be determined and the imaging procedure can be started. This can take from a few minutes to 10 minutes or longer depending on the magnification used in relation to the sample size. -Image analysis: No real human interaction is needed here.

Computing Time Generating and processing datasets - Requirements in computing time

-Digitization procedure: The imaging procedure takes only up to a few minutes. Depending on the workstation (RAM memory and GPU), the stitching procedure takes a couple of minutes. The images are stitched per Z-height. The stacking is done using Zerene stacker. The images are stacked automatic using the Zerene Stacker software using the PMax option. This can be done while picturing a new specimen or overnight. -Image analysis: The camera is usually calibrated before an imaging sequence each day.

Equipment Cost (€) Approximate cost of the setup (integer value)

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Contents

Surveyor User Guide.pdf
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