Difference between revisions of "Slicer3:VisualBlog"

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<gallery caption="2008" widths="200px" perrow="6">
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<gallery caption="2010" widths="200px" perrow="4">
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Image:Gimias-running-slicer-module-2010-10-20.png | A set of slicer command line modules are now shipped as part of the [http://www.gimias.org Gimias] tool from UPF in Barcelona!
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Image:800px-NDI booth Slicer MICCAI2010.jpg | Northern Digital, makers of tracking systems widely used in image guided therapy, used Slicer and OpenIGTLink in their booth installation at [http://www.miccai2010.org/ MICCAI2010 in Beijing].
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Image:prostate_multiparametric_visualization.png | In this screenshot [[Modules:MainApplicationGUI-Documentation-3.6#Selecting_Among_Standard_Layouts|CompareView layout of 3D Slicer]] is used to facilitate visualization of multiparametric MRI of the prostate
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Image:vervet_atlas_template.png| [http://www.nitrc.org/projects/vervet_atlas Vervet Probabilistic Atlas] constructed using 3D Slicer tools is available for download from NITRC.
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Image:Avf 3d voronoi big.png| A Voronoi diagram used for [[Modules:VMTKCenterlines|centerline computation]] of a vascular tree.
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Image:Vmtkaftercenterline.png| [[Modules:VMTKEasyLevelSetSegmentation|Level-set segmentation]] was used to segment this right coronary artery.
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Image:Slicer3.6MeasurementsRulersModel.jpg| [[Modules:Measurements-Documentation-3.6|Rulers and angle widgets]] are available for measuring distances and angles in the 3D scene
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Image:deformable_registration_Screenshot1.png| Non-rigid registration module in 3D Slicer can be used to fuse pre-procedural MR images and intra-procedural CT images during cryoablation of renal tumors. The non-rigid registrations are more accurate than rigid registrations.
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Image:FourDImage_Screenshot1.png|[[Modules:FourDImage-Documentation-3.6|The 4D Image module]] allows handling a time-series of 3D volume images (4D image), e.g. fMRI, cardiac images, dynamic contrast-enhanced (DCE) images in 3D Slicer.
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Image:FourDAnalysisModuleScreenShot-3.5.png|Screenshot of [[Modules:FourDAnalysis-Documentation-3.6|4D Analysis Module]] for lung perfusion data. The module provides functionality to analyze time-intensity curves in specified regions.
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Image:LipsMuscles.png|Three-dimensional appearance of the lip muscles with three-dimensional isotropic MRI: An in vivo study. R. Olszewski, Y. Liu, T. Duprez, T.M. Xu, H. Reychler: Int J Comput Assist Radiol Surg. 2009 Jun;4(4):349-52. [http://www.slicer.org/slicerWeb/images/4/45/Olszewski-IJCARS2009.pdf See here for the pdf]
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Image:RegistrationUsability.png|[[Slicer3:Registration#Registration_in_3D_Slicer|Usability of registration algorithms]]: A joint effort between NA-MIC and NAC is aimed at making advanced registration technology easier to use through better documentation, a solution library and a slicer based solution service.
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Image:ScalarBar.png|[[Modules:Colors-Documentation-3.6|A scalar bar]] is available from the colors module
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Image:LesionsWithVentricles.png|[[Modules:LesionSegmentationApplications-Documentation-3.6|White matter lesion segmentation]] is now available as an extension to Slicer
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Image:RssVentricle.png|[[Modules:RobustStatisticsSeg-Documentation-3.6|RSS]] a new interactive segmentation algorithm
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Image:GPUVolumeRender1.png|With [http://vtk.org VTK version 5.6] blazing fast new hardware accelerated volume rendering is available in slicer nightly builds (require nVidia drivers, available on Windows and Linux only).  This renderer will be available in Slicer 3.6.
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Image:Fastmarching-result-adjusted.jpg|[[Modules:FastMarchingSegmentation-Documentation-3.6|FastMarching segmentation module]] in Slicer 3.6: Segmentation of a meningioma
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Image:Corticalthickness.png| Result from the [[Modules:ARCTIC-Documentation-3.6|ARCTIC module]] in Slicer 3.6: cortical thickness map from pediatric MRI
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Image:SynchroGrab4D titleShot.jpg|[http://hdl.handle.net/10380/3083 SynchroGrab4D] reconstructs 4D (3D+time) ultrasound datasets in real-time, using a tracked 2D transducer.  It is particularly useful for intraoperative imaging of moving organs, including the heart and those influenced by respiratory motion, such as the liver.
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Image:ExtractSubvolumeROI_gallery.png|[[Modules:CropVolume-Documentation-3.6|CropVolume is a new interactive GUI module in Slicer 3.6]] that allows to extract and resample an arbitrary parallelepiped shaped region from a larger scalar image volume.
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Image:ProstateNav_gallery.png|[[Modules:ProstateNav-Documentation-3.6|ProstateNav]] is an interactive GUI module in Slicer 3.6 for MRI guided robot assisted biopsy of the prostate. It supports multiple needle positioning devices: transrectal and transperineal robot and transperineal template.
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Image:RegistrationResults2.jpg| [[Modules:DeformableB-SplineRegistration-Documentation-3.6|B-Spline Registration]] in Slicer 3.6 allows for non-rigid registration between pre-procedure MRI and intra-procedure CT images during CT guided tumor ablation in the liver. It provides increased tumor visualization during the planning, targeting and monitoring phases of the ablation procedure.
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Image:IntraOpDTI.jpg| Intra-operative querying of white matter tracts is now possible by interfacing Slicer 3.6 to the commercial [http://www.brainlab.com/scripts/website_english.asp BrainLab] system and Yale's [http://bioimagesuite.org/ BioImageSuite] software.
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Image:BetaProbe.jpg| Intra-operative navigation of a positron probe can help detect regions of high [18F]-FDG uptake, potentially improving tumor removal at resection borders. The first two image shows a PET/CT scan of the phantom showing where radiation is located, and the third image shows results as indicated by the positron probe.
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</gallery>
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<gallery caption="2009" widths="200px" perrow="4">
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Image:Konnectivity-2009-12-23.png|A frame from [http://aokhok.unideb.hu/konnektivity/ Andras Jakab's interactively zoomable super high-res tractography image!]
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Image:Qt-CLI-2009-11-29.png|Frame from a movie showing Qt Command Line Modules.  See whole movie [http://www.youtube.com/watch?v=e_T2cYGZmSw on youtube].
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Image:Qt-KWW-Transforms-2009-11-24.png|Frame from a movie showing Qt Transforms module. See whole movie [http://www.youtube.com/watch?v=oJFSJWBUFEI on youtube] or download [[file:QSlicerTransformsModule.ogg]].
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Image:VolumeRenderingICPE.png|Volume rendering: Illustrative Context Preserving Exploration
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Image:Dual 3D View.png|Multiple 3D rendering windows
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Image:QMRMLWidgetPlugins-Screenshot.png|Early results of the [[Qt_in_Slicer3]] effort showing new QMRMLWidgets as a plug-in for the QtDesigner application.
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Image:Nagy-simicircular-canals-2009.png|Attila Nagy and his colleagues created a [http://www.orl.szote.u-szeged.hu/~attila/presentations.html very nice set of presentations and animations] with slicer to illustrate 3D reconstruction as applied to otorhinolaryngology.  (See [[Nagy-videos-2009:Notes|Notes]]).
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Image:Slicer3-mac-64bit-2009-09-11.mov|Interactive volume rendering of 512x512x1749 CT volume on 64 bit build of slicer for Mac OSX 10.6.
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Image:Registration-module-hierarchy-prototype.png|Proptype hierarchy of registration modules for specific use-cases that present a simpler view of the capabilities of RegisterImages.
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Image:Xoran-Cone-beam-CT_Craniofacial_Asymetry-2009-08-27.png|Example experiment in craniofacial surgery planning by mirroring one side of the skull to the other.  This example was done in collaboration with Will van Kampen of [http://xorantech.com Xoran Technologies] and was a follow up to the August 25 [http://www.na-mic.org/Wiki/index.php/Events:Slicer_Workshop_August_2009 Slicer IGT Workshop] in Boston.
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Image:Bioimagesuite slicer1.png|[http://www.bioimagesuite.org BioImageSuite] module being discovered.
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Image:Bioimagesuite slicer2.png|[http://www.bioimagesuite.org BioImageSuite] modules in menu.
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Image:Bioimagesuite slicer3.png|Autogenerated [http://www.bioimagesuite.org BioImageSuite] module GUI.
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Image:Bioimagesuite slicer4.png|Slicer command line module recognized and loaded in [http://www.bioimagesuite.org BioImageSuite].
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Image:BIS-Slicer-2009-08-13.jpg|Xenios Papademetris enabled the tools in [http://www.bioimagesuite.org BioImageSuite] to work as command line modules in slicer.
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Image:2009JuneJulyStats.png|See [http://www.slicer.org/pages/Special:Download_Stats?order=downloads&reverse=1 here] for download statistics (page might take a while to load). The Piechart demonstrates the download proportions between the different OS.
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Image:Stochastic-Tractography-01040-lh-all-3D-cropped.png|[http://www.na-mic.org/Wiki/index.php/Summer2009:VCFS '''New Stochastic Tractography'''] tools for analysis of diffusion volumes implemented as Python modules by Julien de Siebenthal.
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Image:3DSlicerFourDAnalysis Screenshot.png |[http://www.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_4D_Imaging '''Four Dimensional Image (Time Series) Analysis'''] Junichi Tokuda has implemented a slicer module for dynamic MR analysis and a general framework for working with time series volume groups.
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Image:Slicer dti seeding or.jpg|[http://www.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_Slicer3_Brainlab_Introduction '''Intraoperative navigation experiments'''] integrate slicer3 with the commercial [http://www.brainlab.com/scripts/website_english.asp BrainLab] system and Yale's [http://bioimagesuite.org/ BioImageSuite] software.
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Image:SkullStrippingInSlicer.png|'''New [http://www.na-mic.org/Wiki/index.php/2009_Summer_Project_Week_Skull_Stripping skull stripping extension module]''' implemented by Xiaodong Tao.
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Image:MS-TSA-CompareView.png|'''CompareView for Longitudinal Visualization of MS''' implemented by Jim Miller and demonstrated using a set of 5 scans of a patient with multiple sclerosis.  Data provided by Dominik Meier of the [http://cni.bwh.harvard.edu Center for Neurological Imaging]
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</gallery>
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<gallery caption="2008" widths="200px" perrow="4">
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Image:Synarc-Li-Level tracing.gif|'''Constrained Level Tracing Algorithm''' implemented by Andrew Li and his team at [http://synarc.com/ Synarc] built on the Slicer3 Editor module has been deployed for bone density measurements in support of clinical trials.  Synarc employees participated in the [http://www.na-mic.org/Wiki/index.php/Stanford_2008_Slicer_Workshop 2008 Slicer Training] event at Stanford University.
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Image:DebrecenTumorMovieStartFrame.png|'''Start frame from [[Tumor_Movie_from_Debrecen|time lapse movie]] showing "Chameleon Tumor" progression.'''  Video courtesy by Ervin Berenyi and Andras Jakab, Department of Medical Laboratory and Diagnostic Imaging, University of Debrecen Medical School and Health Science Center.
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Image:Femesh-in-trunk-120808.png|'''Image showing the [http://www.na-mic.org/Wiki/index.php/NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development IA-FEMesh] module in Slicer3.''' <br> This image shows the display of material properties assigned to a hexahedral mesh. This image was created by Curl Lisle, Nicole Grosland, Kiran Shivanna, Steve Pieper, and Vincent Magnotta
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Image:VascularLesionSegmentation.jpg|'''Image showing the segmentation of vasular lesions based on T1, T2 and FLAIR images.'''<br>A Bayesian classification is performed to label each of the voxels as grey matter, white matter, CSF, and lesion.
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Image:ClipModel-with-widget.png|The new Clip Model Module (Alex Yarmarkovich) uses a VTK box widget to select cutting planes to clip a selected model.
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Image:PythonDistanceTransform.png|Distance Transform from a label map calculated by Steve Pieper using the NumpyScript module created by Luca Antiga. See [[Slicer3:Python]] for more info.
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Image:DTI-Visualization-Neurosurgical-Tutorial.png|Exploring DTI visualization using the [http://wiki.na-mic.org/Wiki/index.php/Slicer3.2:Training Neurosurgical Tutorial]. A virtual probe (fiducial) was positioned in the motor cortex and used as a seed for tractography. The region adjacent to the tumor was used as a seeding area for a separate tractography, which is represented as thin lines with ellipsoid glyphs.
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Image:Color-image-reslice-2008-06-11.png|'''Color Image Reslice''' Demonstrates the ability to read a sequence of jpg files as a color volume and apply 3D interactive reslice tools.  Image data is Visible Human 2 courtesy of the [http://nac.spl.harvard.edu/pages/Research_Cores#Clinical_Computational_Anatomy_Core NAC Clinical Computational Anatomy Core]
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Image:Andras-Jakab-Debrecen-gamma01.jpg|'''Planning for CT Radiosurgery augmented with diffusion tractography (fibers: internal capsule, corpus callosum and the environment of the tumor, which is a metastatic tumor in the parietal lobe)''' Image Courtesy of University of Debrecen, Medical School and Health Science Center [[Debrecen | more information...]]
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Image:Debrecen slicer 01.jpg|'''Integration of diffusion and structural imaging for tumor visualization''' Image Courtesy of University of Debrecen, Medical School and Health Science Center
 
Image:Slicer_IGTL_NITRobot.jpg|'''Integration of Neurosurgical Robot and Slicer using OpenIGTLink, February 2008'''<br>Joint team of Nagoya Institute of Technology and Brigham and Women's Hospital demonstrated a prototype integration of neurosurgical robot and 3D Slicer using OpenIGTLink.
 
Image:Slicer_IGTL_NITRobot.jpg|'''Integration of Neurosurgical Robot and Slicer using OpenIGTLink, February 2008'''<br>Joint team of Nagoya Institute of Technology and Brigham and Women's Hospital demonstrated a prototype integration of neurosurgical robot and 3D Slicer using OpenIGTLink.
 
Image:Cardioseg+volume.png|'''Cardiac segmentation and CT Volume Rendering, February 2008'''<br> Using data and segmentations from the [http://wiki.na-mic.org/Wiki/index.php/NA-MIC_Childrens_Collaboration collaboration with Boston Children's Hospital Pediatric Cardiology].
 
Image:Cardioseg+volume.png|'''Cardiac segmentation and CT Volume Rendering, February 2008'''<br> Using data and segmentations from the [http://wiki.na-mic.org/Wiki/index.php/NA-MIC_Childrens_Collaboration collaboration with Boston Children's Hospital Pediatric Cardiology].
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Image:Slicer_TrackerDaemon_IGSTK.png|'''Image from Haiying Liu, Patrick Cheng, Noby Hata, Junichi Tokuda, Luis Ibanez, and Steve Pieper, January 2008.''' <br>In the NAMIC All Hands Meeting 2008, the bi-directional socket communication has been established between the Tracker Daemon in Slicer 3 and IGSTK server which acquires tracking data from device and sends it to Tracker Daemon. The speed of communication is controlled by Slicer.
 
Image:Slicer_TrackerDaemon_IGSTK.png|'''Image from Haiying Liu, Patrick Cheng, Noby Hata, Junichi Tokuda, Luis Ibanez, and Steve Pieper, January 2008.''' <br>In the NAMIC All Hands Meeting 2008, the bi-directional socket communication has been established between the Tracker Daemon in Slicer 3 and IGSTK server which acquires tracking data from device and sends it to Tracker Daemon. The speed of communication is controlled by Slicer.
 
</gallery>
 
</gallery>
<gallery caption="2007">
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<gallery caption="2007" widths="200px" perrow="4">
 
Image:ENT.png|'''Image from Jaesung Hong December 2007'''<br> Visualization of cochlea(green) and facial nerve(red) for ENT navigation. We are moving on from Slicer2 to Slicer3 at Kyushu University Hospital in Japan.
 
Image:ENT.png|'''Image from Jaesung Hong December 2007'''<br> Visualization of cochlea(green) and facial nerve(red) for ENT navigation. We are moving on from Slicer2 to Slicer3 at Kyushu University Hospital in Japan.
 
Image:Slicer-igstk.png|'''Image from Steve Pieper, Luis Ibanez, Haiying Liu December 2007'''<br>Result of [http://wiki.na-mic.org/Wiki/index.php/2007_December_Slicer_IGT_Programming Slicer for IGT workshop] showing Slicer3 transform node being updated by a [http://www.igstk.org IGSTK] tracker process.
 
Image:Slicer-igstk.png|'''Image from Steve Pieper, Luis Ibanez, Haiying Liu December 2007'''<br>Result of [http://wiki.na-mic.org/Wiki/index.php/2007_December_Slicer_IGT_Programming Slicer for IGT workshop] showing Slicer3 transform node being updated by a [http://www.igstk.org IGSTK] tracker process.
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Image:Slicer3FirstTractography.png|'''Image from pieper on Tuesday, January 16, 2007 at  7:58PM'''<br>From Lauren, shows fiber tracts loaded from a file and with display properties controlled by the GUI.
 
Image:Slicer3FirstTractography.png|'''Image from pieper on Tuesday, January 16, 2007 at  7:58PM'''<br>From Lauren, shows fiber tracts loaded from a file and with display properties controlled by the GUI.
 
</gallery>
 
</gallery>
<gallery caption="2006">
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<gallery caption="2006" widths="200px" perrow="4">
 
Image:S3GUI-12-29-06.png|'''Image from wjp on Friday, December 29, 2006 at 3:23PM'''<br>Module choose and navigation functionality integrated into the application toolbar to create more space for module GUIs on the side panel. Slice Controller widgets also updated to have more functionality available, a button to link and unlink their control, and an improved visual design.
 
Image:S3GUI-12-29-06.png|'''Image from wjp on Friday, December 29, 2006 at 3:23PM'''<br>Module choose and navigation functionality integrated into the application toolbar to create more space for module GUIs on the side panel. Slice Controller widgets also updated to have more functionality available, a button to link and unlink their control, and an improved visual design.
 
Image:S3GUIWithLogo.png|'''Image from wjp on Monday, November 28, 2006 at 6:40M'''<br>New 3D Slicer logo integrated with slicer GUI.
 
Image:S3GUIWithLogo.png|'''Image from wjp on Monday, November 28, 2006 at 6:40M'''<br>New 3D Slicer logo integrated with slicer GUI.

Latest revision as of 23:18, 2 July 2011

Home < Slicer3:VisualBlog



About the VisualBlog

The VisualBlog is meant to be an easy place to upload screenshot so that both developers and outside observes can track the progress of the project.

Many thanks to developers and users for contributing their images here.