Integrating XMALab and DeepLabCut for high-throughput XROMM

Mapping Intimacies ◽

10.1101/2020.04.10.035949 ◽

2020 ◽

Author(s):

JD Laurence-Chasen ◽

AR Manafzadeh ◽

NG Hatsopoulos ◽

CF Ross ◽

FI Arce-McShane

Keyword(s):

Large Scale ◽

Fold Increase ◽

X Ray ◽

Marker Tracking ◽

Markerless Tracking ◽

Automatic Batch ◽

Major Bottleneck ◽

Proper Context

ABSTRACTMarker tracking is a major bottleneck in studies involving X-ray Reconstruction of Moving Morphology (XROMM). Here, we tested whether DeepLabCut, a new deep learning package built for markerless tracking, could be applied to videoradiographic data to improve data processing throughput. Our novel workflow integrates XMALab, the existing XROMM marker tracking software, and DeepLabCut while retaining each program’s utility. XMALab is used for generating training datasets, error correction, and 3D reconstruction, whereas the majority of marker tracking is transferred to DeepLabCut for automatic batch processing. In the two case studies that involved an in vivo behavior, our workflow achieved a 6 to 13-fold increase in data throughput. In the third case study, which involved an acyclic, post mortem manipulation, DeepLabCut struggled to generalize to the range of novel poses and did not surpass the throughput of XMALab alone. Deployed in the proper context, this new workflow facilitates large scale XROMM studies that were previously precluded by software constraints.

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Integrating XMALab and DeepLabCut for high-throughput XROMM

Journal of Experimental Biology ◽

10.1242/jeb.226720 ◽

2020 ◽

Vol 223 (17) ◽

pp. jeb226720

Author(s):

J.D. Laurence-Chasen ◽

Armita R. Manafzadeh ◽

Nicholas G. Hatsopoulos ◽

Callum F. Ross ◽

Fritzie I. Arce-McShane

Keyword(s):

Large Scale ◽

Fold Increase ◽

X Ray ◽

Marker Tracking ◽

Markerless Tracking ◽

Automatic Batch ◽

Major Bottleneck ◽

Proper Context

ABSTRACTMarker tracking is a major bottleneck in studies involving X-ray reconstruction of moving morphology (XROMM). Here, we tested whether DeepLabCut, a new deep learning package built for markerless tracking, could be applied to videoradiographic data to improve data processing throughput. Our novel workflow integrates XMALab, the existing XROMM marker tracking software, and DeepLabCut while retaining each program's utility. XMALab is used for generating training datasets, error correction and 3D reconstruction, whereas the majority of marker tracking is transferred to DeepLabCut for automatic batch processing. In the two case studies that involved an in vivo behavior, our workflow achieved a 6 to 13-fold increase in data throughput. In the third case study, which involved an acyclic, post-mortem manipulation, DeepLabCut struggled to generalize to the range of novel poses and did not surpass the throughput of XMALab alone. Deployed in the proper context, this new workflow facilitates large scale XROMM studies that were previously precluded by software constraints.

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Multi-marker tracking for large-scale X-ray stereo video data

Signal Processing Image Communication ◽

10.1016/j.image.2017.06.009 ◽

2017 ◽

Vol 59 ◽

pp. 140-149 ◽

Cited By ~ 1

Author(s):

Xiaoyan Jiang ◽

Marcel Simon ◽

Yuan Yang ◽

Joachim Denzler

Keyword(s):

Large Scale ◽

Video Data ◽

X Ray ◽

Marker Tracking ◽

Stereo Video

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Flux-Based Formulation Development—A Proof of Concept Study

The AAPS Journal ◽

10.1208/s12248-021-00668-9 ◽

2022 ◽

Vol 24 (1) ◽

Author(s):

Szabina Kádár ◽

Petra Tőzsér ◽

Brigitta Nagy ◽

Attila Farkas ◽

Zsombor K. Nagy ◽

...

Keyword(s):

Large Scale ◽

Small Volume ◽

Drug Product ◽

Dosage Forms ◽

Drug Formulation ◽

Screening Methods ◽

Formulation Development ◽

First Case

AbstractThe work aimed to develop the Absorption Driven Drug Formulation (ADDF) concept, which is a new approach in formulation development to ensure that the drug product meets the expected absorption rate. The concept is built on the solubility-permeability interplay and the rate of supersaturation as the driving force of absorption. This paper presents the first case study using the ADDF concept where not only dissolution and solubility but also permeation of the drug is considered in every step of the formulation development. For that reason, parallel artificial membrane permeability assay (PAMPA) was used for excipient selection, small volume dissolution-permeation apparatus was used for testing amorphous solid dispersions (ASDs), and large volume dissolution-permeation tests were carried out to characterize the final dosage forms. The API-excipient interaction studies on PAMPA indicated differences when different fillers or surfactants were studied. These differences were then confirmed with small volume dissolution-permeation assays where the addition of Tween 80 to the ASDs decreased the flux dramatically. Also, the early indication of sorbitol’s advantage over mannitol by PAMPA has been confirmed in the investigation of the final dosage forms by large-scale dissolution-permeation tests. This difference between the fillers was observed in vivo as well. The presented case study demonstrated that the ADDF concept opens a new perspective in generic formulation development using fast and cost-effective flux-based screening methods in order to meet the bioequivalence criteria.

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Large-Scale Synthesis of Bi2S3Nanodots as a Contrast Agent for In Vivo X-ray Computed Tomography Imaging

Advanced Materials ◽

10.1002/adma.201103289 ◽

2011 ◽

Vol 23 (42) ◽

pp. 4886-4891 ◽

Cited By ~ 234

Author(s):

Kelong Ai ◽

Yanlan Liu ◽

Jianhua Liu ◽

Qinghai Yuan ◽

Yangyang He ◽

...

Keyword(s):

Computed Tomography ◽

Contrast Agent ◽

Large Scale ◽

Computed Tomography Imaging ◽

X Ray ◽

Tomography Imaging ◽

X Ray Computed ◽

Large Scale Synthesis

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Large-Scale and Facile Synthesis of Biocompatible Yb-Based Nanoparticles as a Contrast Agent for In Vivo X-Ray Computed Tomography Imaging

Current Topics in Medicinal Chemistry ◽

10.2174/1568026611313040011 ◽

2013 ◽

Vol 13 (4) ◽

pp. 513-518 ◽

Cited By ~ 5

Author(s):

Jianhua Liu ◽

Rui Xin ◽

Zhiman Li ◽

Reza Golamaully ◽

Yan Zhang ◽

...

Keyword(s):

Computed Tomography ◽

Contrast Agent ◽

Large Scale ◽

Facile Synthesis ◽

Computed Tomography Imaging ◽

X Ray ◽

Tomography Imaging ◽

X Ray Computed

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EFFECT OF CAPTOPRIL

The Professional Medical Journal ◽

10.29309/tpmj/2012.19.01.1929 ◽

2012 ◽

Vol 19 (01) ◽

pp. 078-085

Author(s):

MISS GULL- E-FARAN ◽

MUHAMMAD ANJUM ZIA ◽

NIGHAT ASLAM

Keyword(s):

Large Scale ◽

Thiobarbituric Acid ◽

Inhibitory Effect ◽

Effective Concentration ◽

Diabetic Patients ◽

Total Proteins ◽

Design Case Study ◽

One Year

Objectives: (1) To investigate the inhibitory effect of Captopril on level of glycation (in vivo). (2) To study glycation inhibition invivo. Study design: Case study. Period: Sep. 2006 to March. 2008. One year seven months. Setting: Department of Biochemistry Universityof Agriculture, Faisalabad. Methods: Different parameters like fluorescence, total proteins, TBA (thiobarbituric acid) method, periodateborohydride assay were used to check the effect of inhibitor on glycation. Thirty two combinations were made and all these combinations wereplaced at 37̊C, at same time for five weeks. 3mL of blood sample was drawn after 1st, 3rd and 5th week of incubation to perform the experimentsfor glycation and glycation inhibition. Along with the same temperature (37̊C), different combinations of glucose and inhibitor were used.Results: Effective concentration of inhibitor helped to decrease the level of glycation. All concentrations of glucose (G , G and G ) showed 1 2 3glycation with protein. The inhibitor Captopril (all concentrations) showed variations in inhibition of glycation at one temperature (37̊C) withdifferent parameters (Fluorescence, TBA and Periodate) but the most effective concentration of inhibitors at each condition is I (1mM) but I (10 3 1mM) and I (5 mM) were also equally effective after I . Periodate borohydride Assay is more effective for glycation determination than 2 3thiobarbituric acid assay. Conclusions: Captopril can be used as glycation inhibitor in future. As it enhances the activity of transketolase, it canproduce 3DG compound which can block the AGEs. However, more experimentations should be done on animal or on large scale before itsapplication in diabetic patients.

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Preparation of cultured astrocytes for x-ray microanalysis

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100156924 ◽

1989 ◽

Vol 47 ◽

pp. 988-989

Author(s):

N.K.R. Smith ◽

K.E. Hunter ◽

P. Mobley ◽

L.P. Felpel

Keyword(s):

Cultured Cells ◽

Elemental Content ◽

Elemental Distribution ◽

Sprague Dawley ◽

X Ray ◽

Cultured Astrocytes ◽

Freeze Dried ◽

Ultimate Objective

Electron probe energy dispersive x-ray microanalysis (XRMA) offers a powerful tool for the determination of intracellular elemental content of biological tissue. However, preparation of the tissue specimen , particularly excitable central nervous system (CNS) tissue , for XRMA is rather difficult, as dissection of a sample from the intact organism frequently results in artefacts in elemental distribution. To circumvent the problems inherent in the in vivo preparation, we turned to an in vitro preparation of astrocytes grown in tissue culture. However, preparations of in vitro samples offer a new and unique set of problems. Generally, cultured cells, growing in monolayer, must be harvested by either mechanical or enzymatic procedures, resulting in variable degrees of damage to the cells and compromised intracel1ular elemental distribution. The ultimate objective is to process and analyze unperturbed cells. With the objective of sparing others from some of the same efforts, we are reporting the considerable difficulties we have encountered in attempting to prepare astrocytes for XRMA.Tissue cultures of astrocytes from newborn C57 mice or Sprague Dawley rats were prepared and cultured by standard techniques, usually in T25 flasks, except as noted differently on Cytodex beads or on gelatin. After different preparative procedures, all samples were frozen on brass pins in liquid propane, stored in liquid nitrogen, cryosectioned (0.1 μm), freeze dried, and microanalyzed as previously reported.

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A Family With Autosomal-Dominant Progressive Sensorineural Hearing Loss

American Journal of Audiology ◽

10.1044/1059-0889.0501.23 ◽

1996 ◽

Vol 5 (1) ◽

pp. 23-32 ◽

Cited By ~ 3

Author(s):

Chris Halpin ◽

Barbara Herrmann ◽

Margaret Whearty

Keyword(s):

Speech Production ◽

Hearing Aids ◽

Role Models ◽

Speech Intelligibility ◽

Large Scale ◽

Speech Language Pathology ◽

The Family ◽

Patient Will ◽

Language Pathology

The family described in this article provides an unusual opportunity to relate findings from genetic, histological, electrophysiological, psychophysical, and rehabilitative investigation. Although the total number evaluated is large (49), the known, living affected population is smaller (14), and these are spread from age 20 to age 59. As a result, the findings described above are those of a large-scale case study. Clearly, more data will be available through longitudinal study of the individuals documented in the course of this investigation but, given the slow nature of the progression in this disease, such studies will be undertaken after an interval of several years. The general picture presented to the audiologist who must rehabilitate these cases is that of a progressive cochlear degeneration that affects only thresholds at first, and then rapidly diminishes speech intelligibility. The expected result is that, after normal language development, the patient may accept hearing aids well, encouraged by the support of the family. Performance and satisfaction with the hearing aids is good, until the onset of the speech intelligibility loss, at which time the patient will encounter serious difficulties and may reject hearing aids as unhelpful. As the histological and electrophysiological results indicate, however, the eighth nerve remains viable, especially in the younger affected members, and success with cochlear implantation may be expected. Audiologic counseling efforts are aided by the presence of role models and support from the other affected members of the family. Speech-language pathology services were not considered important by the members of this family since their speech production developed normally and has remained very good. Self-correction of speech was supported by hearing aids and cochlear implants (Case 5’s speech production was documented in Perkell, Lane, Svirsky, & Webster, 1992). These patients received genetic counseling and, due to the high penetrance of the disease, exhibited serious concerns regarding future generations and the hope of a cure.

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