Merge pull request #11 from PyTomography/development

add tests

Author: lukepolson

docs/source/tutorials/1_kernel1d_intro.ipynb

@@ -226,4 +226,101 @@ @article{ac6
   pages={2504--2514},
   year={2024},
   doi={10.1007/s00259-024-06681-2}
-}
+}
+
+@article{GRF_2,
+doi = {10.1088/0031-9155/35/1/008},
+url = {https://dx.doi.org/10.1088/0031-9155/35/1/008},
+year = {1990},
+month = {jan},
+publisher = {},
+volume = {35},
+number = {1},
+pages = {81},
+author = {B M W Tsui and  G T Gullberg},
+title = {The geometric transfer function for cone and fan beam collimators},
+journal = {Physics in Medicine & Biology},
+abstract = {Geometric response functions are derived for both cone and fan beam collimators for the scintillation camera. The formulation is based on an effective response function which is determined by the geometric response of a single hole. The technique provides an accurate description of the spatial resolution by characterising the complete geometric response function which includes the effects of the shape and orientation of the collimator holes. The theoretical formulation was used to design a fan beam collimator for SPECT imaging and was shown to agree well with the experimental results.}
+}
+
+@article{GRF_3,
+doi = {10.1088/0031-9155/43/4/021},
+url = {https://dx.doi.org/10.1088/0031-9155/43/4/021},
+year = {1998},
+month = {apr},
+publisher = {},
+volume = {43},
+number = {4},
+pages = {941},
+author = {E C Frey and  B M W Tsui and  G T Gullberg},
+title = {Improved estimation of the detector response function for converging beam collimators},
+journal = {Physics in Medicine & Biology},
+abstract = {Converging beam collimator geometries offer improved tradeoffs between resolution and noise for single photon emission computed tomography (SPECT). The major factor limiting the resolution in SPECT is the collimator-detector response blurring. In order to compensate for this blurring it is useful to be able to calculate the collimator response function. A previous formulation presented a method for calculating the response for parallel and converging beam collimators that assumed that the shape of the holes did not change over the face of the collimator. However, cast collimators are fabricated using pins with a constant cross-section (shape perpendicular to the pin axis). As a result, due to the angulation of the pins, the holes made by these pins have shapes on the front and back faces of the collimator that change with position. This change in hole shape is especially pronounced when the angle between the collimator hole and the collimator normal is large, as is the case for half-fan-beam or short-focal-length collimators. This paper presents a derivation of a modification to the original method that accounts for the change in shape of the collimator holes. The method has been verified by comparing predicted line spread functions to experimentally measured ones for a collimator with a maximum hole angle of  with respect to the normal. This formulation is useful for predicting the response of fan-beam collimators in the design process and for use in detector response compensation algorithms.}
+}
+
+@article{GRF_4,
+doi = {10.1088/0031-9155/43/11/013},
+url = {https://dx.doi.org/10.1088/0031-9155/43/11/013},
+year = {1998},
+month = {nov},
+publisher = {},
+volume = {43},
+number = {11},
+pages = {3359},
+author = {Andreas Robert Formiconi},
+title = {Geometrical response of multihole collimators},
+journal = {Physics in Medicine & Biology},
+abstract = {A complete theory of camera multihole collimators is presented. The geometrical system response is determined in closed form in frequency space. This closed form accounts for the known efficiency and resolution formulae for parallel beam, fan beam, cone beam and astigmatic collimators as well as for the most frequent hole array patterns and hole shapes. The point spread function in the space domain for a certain collimator and source position can be calculated via a discrete fast Fourier transform. Beside the complete theoretical definition of the response of multihole collimators, this theory allows the definition of accurate models of the geometrical response for SPECT reconstruction and it is suitable for designing new collimators.}
+}
+
+@article{metz1980geometric,
+  title={The geometric transfer function component for scintillation camera collimators with straight parallel holes},
+  author={Metz, C E and Atkins, F B and Beck, R N},
+  journal={Physics in Medicine and Biology},
+  volume={25},
+  number={6},
+  pages={1059--1070},
+  year={1980},
+  publisher={IOP Publishing},
+  doi={10.1088/0031-9155/25/6/003}
+}
+
+@ARTICLE{septal,
+  author={Du, Y. and Frey, E.C. and Wang, W.T. and Tocharoenchai, C. and Baird, W.H. and Tsui, B.M.W.},
+  journal={IEEE Transactions on Nuclear Science}, 
+  title={Combination of MCNP and SimSET for Monte Carlo simulation of SPECT with medium- and high-energy photons}, 
+  year={2002},
+  volume={49},
+  number={3},
+  pages={668-674},
+  keywords={Single photon emission computed tomography;Computational modeling;Imaging phantoms;Medical simulation;Optical collimators;Particle scattering;Nuclear medicine;Reconstruction algorithms;Electromagnetic scattering;X-ray scattering},
+  doi={10.1109/TNS.2002.1039547}}
+
+@Inbook{Zaidi2006,
+author="Zaidi, H.
+and Hasegawa, B. H.",
+editor="Zaidi, Habib",
+title="Overview of Nuclear Medical Imaging: Physics and Instrumentation",
+bookTitle="Quantitative Analysis in Nuclear Medicine Imaging",
+year="2006",
+publisher="Springer US",
+address="Boston, MA",
+pages="1--34",
+isbn="978-0-387-25444-9",
+doi="10.1007/0-387-25444-7_1",
+url="https://doi.org/10.1007/0-387-25444-7_1"
+}
+
+@article {bi213_amyloid,
+	author = {Bender, Aidan A. and Kirkeby, Emily K. and Cross, Donna J. and Minoshima, Satoshi and Roberts, Andrew G. and Mastren, Tara E.},
+	title = {Development of a 213Bi-Labeled Pyridyl Benzofuran for Targeted α-Therapy of Amyloid-β Aggregates},
+	elocation-id = {jnumed.124.267482},
+	year = {2024},
+	doi = {10.2967/jnumed.124.267482},
+	publisher = {Society of Nuclear Medicine},
+	abstract = {Alzheimer disease is a neurodegenerative disorder with limited treatment options. It is characterized by the presence of several biomarkers, including amyloid-β aggregates, which lead to oxidative stress and neuronal decay. Targeted α-therapy (TAT) has been shown to be efficacious against metastatic cancer. TAT takes advantage of tumor-localized α-particle emission to break disease-associated covalent bonds while minimizing radiation dose to healthy tissues due to the short, micrometer-level, distances traveled. We hypothesized that TAT could be used to break covalent bonds within amyloid-β aggregates and facilitate natural plaque clearance mechanisms. Methods: We synthesized a 213Bi-chelate{\textendash}linked benzofuran pyridyl derivative (BiBPy) and generated [213Bi]BiBPy, with a specific activity of 120.6 GBq/μg, dissociation constant of 11 {\textpm} 1.5 nM, and logP of 0.14 {\textpm} 0.03. Results: As the first step toward the validation of [213Bi]BiBPy as a TAT agent for the reduction of Alzheimer disease{\textendash}associated amyloid-β, we showed that brain homogenates from APP/PS1 double-transgenic male mice (6{\textendash}9 mo old) incubated with [213Bi]BiBPy exhibited a marked reduction in amyloid-β plaque concentration as measured using both enzyme-linked immunosorbent and Western blotting assays, with a half-maximal effective concentration of 3.72 kBq/pg. Conclusion: This [213Bi]BiBPy-concentration{\textendash}dependent activity shows that TAT can reduce amyloid plaque concentration in~vitro and supports the development of targeting systems for in~vivo validations.},
+	issn = {0161-5505},
+	URL = {https://jnm.snmjournals.org/content/early/2024/07/25/jnumed.124.267482},
+	eprint = {https://jnm.snmjournals.org/content/early/2024/07/25/jnumed.124.267482.full.pdf},
+	journal = {Journal of Nuclear Medicine}
+}