PiAutoStage: An Open‐Source 3D Printed Tool for the Automatic Collection of High‐Resolution Microscope Imagery

Steiner, R. Alex; Rooney, Tyrone O.

doi:10.1029/2021gc009693

Cited by 7 publications

(5 citation statements)

References 32 publications

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“…For analysis of larger FoVs or WSI, different solutions are possible. At the low‐cost end, the affordable PiAutoStage 104 accessory converts a regular petrographic microscope into a device capable of WSI. If it was expanded with motorised rotation of the light path components, POAM could turn such an instrument into a powerful fabric analyser.…”

Section: Conclusion Summary and Outlookmentioning

confidence: 99%

Using the traditional microscope for mineral grain orientation determination: A prototype image analysis pipeline for optic‐axis mapping (POAM)

Acevedo Zamora,

Schrank,

Kamber

2024

Journal of Microscopy

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This paper reports on the development of an open‐source image analysis software ‘pipeline’ dedicated to petrographic microscopy. Using conventional rock thin sections and images from a standard polarising microscope, the pipeline can classify minerals and subgrains into objects and obtain information about optic‐axis orientation. Five metamorphic rocks were chosen to test and illustrate the method. Thin sections were imaged using reflected and cross‐ and plane‐polarised transmitted light. Images were taken at different angles of the polariser and analyser (360° with 10° steps), both with and without the full‐lambda plate. The resulting image stacks were analysed with a modular pipeline for optic‐axis mapping (POAM). POAM consists of external and internal software packages that register, segment, classify, and interpret the visible light spectra using object‐based image analysis (OBIAS). The mapped fields‐of‐view and grain orientation stereonets of interest are presented in the context of whole‐slide images.Two innovations are reported. First, we used hierarchical tree region merging on blended multimodal images to classify individual grains of rock‐forming minerals into objects. Second, we assembled a new optical mineralogy algorithm chain that identifies the mineral slow axis orientation. The c‐axis orientation results were verified with scanning electron microscopy electron backscattered diffraction (SEM‐EBSD) data. For quartz (uniaxial) in a granite mylonite the test yielded excellent correspondence of c‐axis azimuth and good agreement for inclination. For orthorhombic orthopyroxene in a deformed garnet harzburgite, POAM produced acceptable results for slow axis azimuth. In addition, the method identified slight anisotropy in garnet that would not be appreciated by traditional microscopy.We propose that our method is ideally suited for two commonly performed tasks in mineralogy. First, for mineral grain classification of entire thin sections scans on blended images to provide automated modal abundance estimates and grain size distribution. Second, for prospective fields of view of interest, POAM can rapidly generate slow axis crystal orientation maps from multiangle image stacks on conventionally prepared thin sections for targeting detailed SEM‐EBSD studies.

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Section: Conclusion Summary and Outlookmentioning

confidence: 99%

Using the traditional microscope for mineral grain orientation determination: A prototype image analysis pipeline for optic‐axis mapping (POAM)

Acevedo Zamora,

Schrank,

Kamber

2024

Journal of Microscopy

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“…In lieu of high‐cost metal machining for tight tolerances which are necessary in some applications, researchers now have the option to print custom components where precise tolerances are not critical. We have seen custom open‐source microscope systems aimed at the imaging of microscope slides of rock specimens (Steiner & Rooney, 2021), imaging insects in the life‐sciences domain (Campbell et al., 2014), and highly customizable microscopy systems (Sharkey et al., 2016). Each of these systems has a motorized stage that has two (or three) degrees of freedom and can achieve micron‐level precision.…”

Section: Related Workmentioning

confidence: 99%

“…Each of these systems has a motorized stage that has two (or three) degrees of freedom and can achieve micron‐level precision. Where some require manual intervention for imaging (Campbell et al., 2014; Sharkey et al., 2016), open‐source projects leave room for customization for automated imaging or come with it prepackaged (Steiner & Rooney, 2021). These are all great solutions for general microscopy, but one large drawback when dealing with foraminifera is the need to manually manipulate and orient all the samples, which is time consuming by itself.…”

Section: Related Workmentioning

confidence: 99%

Forabot: Automated Planktic Foraminifera Isolation and Imaging

Richmond

Cole

Dangler

et al. 2022

Geochem Geophys Geosyst

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Foraminifera, or forams for short, are ubiquitous in the world ocean (Sengupta, 1999). Along with their abundance, their biodiversity and extent of geologic record make their fossils of particular interest to paleontologists and paleoclimatologists (Schmiedl, 2019). The sand-sized fraction of deep sea sediments is often dominated by planktic foraminifera, of which there are about 50 extant species (Schiebel & Hemleben, 2017). Although modern benthic foraminiferal species number in the thousands, they are typically only abundant in shallow (shelf) environments and in poorly preserved abyssal sediments. For this work, we focus on deep-sea sediment and as such do not include analysis or commentary on benthic foraminifera. Due to the small size and great abundance of planktic foraminifera, hundreds or possibly thousands can often be picked from a single cubic centimeter of ocean floor mud. Foraminifera samples are normally sorted by species before they are used for either academic or

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“…It's worth noting that the cost of both microscopes exceeds $1000, making them relatively expensive options. In the realm of open-source projects, PiAutoStage [34] also utilizes 3D printing technology to construct a microscope and offers a method for digitizing microscope slides using an automatic stage. Still, they have reported it with only 2x and 4x objective lenses.…”

Section: Introductionmentioning

confidence: 99%

Slide scanning stage: a modular, low-cost, portable, and precise solution for sample analysis in hematology

Hassan,

Javed,

Mahmood

et al. 2024

Optical Design and Engineering IX

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Microscopes are essential tools in research laboratories and hospitals to facilitate the examination of blood samples and other biological materials. As technological advancements continue to reshape the landscape of scientific research, there have been many enhancements in microscopy in terms of efficiency and automation of manual tasks. However, the process of slide scanning remains a labor-intensive task, particularly in developing and underdeveloped countries where access to expensive solutions may be limited. This research paper introduces an affordable 3D printed slide scanning stage equipped with an integratable camera to automate the image-capturing process at high magnification. The system, being powered by Arduino Mega, a versatile microprocessor, can support comprehensive 2D slide scanning with a significant range of motion (75 mm on the x-axis and 25 mm on the y-axis) and manage to drive multiple stepper motors in real-time (resulting in the precision of 3.9 microns per step). Both the area to be scanned and the magnification need to be provided in the code, and it will automatically calculate the remaining stuff to get the job done. There is an optointerrupter sensor that provides feedback for every 166-micron movement of the stage, helping the system to accommodate for step missing or any external jerks during the movement. Furthermore, the user-friendly controls ensure a seamless experience for operators. These features collectively make the 3D printed slide scanning stage a valuable tool for various applications in research and medical settings, promising enhanced portability and precision.

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PiAutoStage: An Open‐Source 3D Printed Tool for the Automatic Collection of High‐Resolution Microscope Imagery

Cited by 7 publications

References 32 publications

Using the traditional microscope for mineral grain orientation determination: A prototype image analysis pipeline for optic‐axis mapping (POAM)

Using the traditional microscope for mineral grain orientation determination: A prototype image analysis pipeline for optic‐axis mapping (POAM)

Forabot: Automated Planktic Foraminifera Isolation and Imaging

Slide scanning stage: a modular, low-cost, portable, and precise solution for sample analysis in hematology

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