Imaris Software For Mac Os 32
Acquisition [top] Hamamatsu Orca 12-bit Camera Shading Corrector QuickTime Capture (Capture images using QuickTime) TWAIN JTwain Twain Scan SensiCam Long Exposure Camera Video Capture Macro Tool(Video for Windows via VirtualDub) Capturing plugin(Captures images on Windows using JMF) Webcam Capture (Video capture on OS X, Linux and Windows) www.qimaging.com:QImaging Firewire Cameras ScionFGAkiz:Scion full-frame-rate capture FWCamAkiz:Mac OS X Firewire Cameras www.pixelsmart.com:PixelSmart Frame Grabbers www.bruxton.com:Andor, Cooke, Hamamatsu, PCO, Princeton Instruments, Photometrics, Red Shirt Imaging and SciMeasure Cameras www.aas2.com:Ann Arbor Sensor Systems AXT100 Thermal Imaging Camera www.pco.de:Cooke PCO, Sensicam and Pixelfly Cameras mbl.edu:CamAcqJ plugin for QImaging Retiga cameras (Windows only) www.fclab.com:FCLabFC1000/2000 USB 2.0 Cameras (Windows only) micro-manager.org(μManager): Open source, multi-platform, extendable; stage, filter wheel and shutter control; serial I/O; Zeiss and Nikon microscopes; Hamamatsu, Andor, PVCAM, DVC and IIDC Firewire cameras; Shutters, stages, etc. by Vincent (Uniblitz), Ludl, Prior, ASI and Sutter PHASE GmbH:Firewire and GigE Vision camera control software (Windows only) CivilCapture:Capture images using theLTI-Civil Java library Lumenera:Infinity USB 2.0 cameras (Mac only) Dage-MTI:Plugin for XLV, XL16 and XLM cameras (Windows only) Jenoptik:Mac and Windows plugins for ProgRes microscope cameras AVerMedia:Plugins for DarkCrystal HD Capture cards (Windows only) iSight Capture: Webcam video capture using JavaCV and OpenCV Videoscan:Plugin for Videoscan camera (Windows only) HF_IDS_Cam:High Frequency IDS Camera Capture (Linux and Windows only)
imaris software for mac os 32
Open the file in FIJI. FIJI (is just ImageJ) is a powerful open-source, free software tool that can open most proprietary file formats and is available for Mac, Linux, and Windows. If you drag your file onto the FIJI status bar, it will use the BioFormats library to open your images as well as display the metadata. Once your data is in FIJI, you can perform 3D visualization and processing of your images and save them in a variety of other formats (eg. .tif, avi, .gif). Sometimes this approach works smoothly, and other times there may be some issues getting the import to work properly. Image.sc is an active discussion forum where you can see if anyone has had similar issues and find potential solutions.
Convert to Imaris format and use the MIC Imaris license. The MIC has an image analysis workstation that has an installation of Imaris, a large-data optimized commercial image analysis software. Imaris converts proprietary microscope image files to .ims files which can be further processed within the software. Commonly used analysis tools include measurement, annotation, object detection, and filament tracing. You can use this software on the workstation at the MIC for $1/hr (max of $8/day), or you can check out a satellite license to use on your own machine for $35/week.
Export as .tif file. When you acquire the images, you can export them as .tif files, but be sure to record the experimental metadata in a secure place. These images can be opened by most image viewing and editing software (eg. FIJI, gimp, photoshop).
The Zeiss Axiophot microscope equipped with a Plan Neofluoar 100x/1.3 oil-immersion objective and a Coolsnap cf camera was used to create a z-stack of GFP fluorescence images with z-step of 0.2 um. The raw image stack was processed with AutoDeblur X software (Media Cybernetics) using 100 iterations of blind deconvolution algorithm, taking into account spherical aberration due to refractive index mismatch. The raw and deconvolved image stacks were then opened in ImageJ software to generate orthogonal views of the image stacks. Note: the large amount of out-of-focus blur in the raw image as well as the improvement in contrast and resolvable detail in the deconvolved dataset. Image data was acquired by Laura Short (Department of Anthropology) during the Spring 2009 Light Microscopy course offered by the MIC. Image processing by Stanislav Vitha, MIC.
Here, we present a new open-source software, Microscopy Image Browser (MIB) , that was designed for, but not limited to, easy and effective segmentation of multidimensional datasets, improving and facilitating the full utilization and quantitation of acquired data. MIB has a user-friendly graphical interface and is available for all common computer operating systems, either together with MATLAB (Windows, Linux, and Mac OS) or as a stand-alone package for Windows and Mac OS. At present, MIB has been utilized in more than ten different scientific projects, ranging from studies at the cellular level to those dealing with whole organisms; examples include projects on the endoplasmic reticulum (ER) and cytoskeletal filaments in cultured cells [10,11], the organ of Corti in mouse inner ear [12,13], the development of the sieve element in Arabidopsis thaliana root [14,15], and the characterization of cryptomonad Rhinomonas nottbecki n. sp. . Although MIB was originally designed for the processing of relatively large EM datasets, it can be used for analysis of LM and any other microscopy datasets. Here, we provide several examples highlighting the various features of the program, and online tutorials have been made to provide detailed instructions on how to use them .
The output files from different microscopes and programs are routinely stored in proprietary formats, and access to the collected images and corresponding metadata after acquisition often requires customized software from the manufacturer. MIB overcomes this problem by offering reading capabilities of up to 100 microscopy image and video formats powered by custom-made MATLAB and Bio-Formats  readers (Fig 1A; see MIB home page for the full list ). MIB was designed as an image browser to allow fast access to individual image datasets for viewing and assembling into 3-D and 4-D stacks (X:Y:Color:Z or X:Y:Color:Time). Up to eight datasets can be simultaneously opened and synchronized, facilitating the comparison and analysis of data from different experiments. The processed images can be exported using most frequently used output formats (Fig 1A).
(A) A screenshot of the MIB user interface. The program menu, toolbar, and panels are highlighted. A brief description of each element is provided. (B) A dedicated website includes direct links for software download and covers various topics and aspects of MIB functionality. Image credit: Ilya Belevich, on behalf of MIB.
Mice were perfused with 4% paraformaldehyde. Mouse brains were removed and post-fixed in 4% PFA for 24 h, followed by immersion in 30% sucrose for 48 h, then embedded in Optimal Cutting Temperature (OCT). 5-μm sections were placed on glass slides and stained with solochrome cyanine to confirm the presence of a lesion as previously described . Sections were stained with the following primary antibodies: Rb anti-dMBP (Millipore, ab5864, 1:2000), Rb anti-Iba1 (Wako, 019-19741, 1:600), Gt anti-Iba1 (Novus, NB100-1028, 1:250), Rt anti-LAMP1 (Abcam, ab25245, 1:500), Rt anti-CD68 (Invitrogen, 14-0681-82, 1:300), Rb anti-PDGFRα (ThermoFisher, PA5-16742, 1:50), Rb anti-OLIG2 (Milipore, AB9610, 1:300), Ms anti-CNPase (Abcam, ab6319, :100), Shp anti-BrdU (Abcam, ab1893, 1:250), Rt anti-GFAP (ThermoFisher, 13-0300, 1:200), and Ms anti-SMI-31 (Biolegend, 801603, 1:1000). AlexaFluor-conjugated secondary antibodies (Invitrogen, 1:1000) were used. Some of the images were acquired with a Nikon Eclipse 90i fluorescent and bright field microscope equipped with 10 and 20 zoom objectives and analyzed with Metamorph 7.7 software. CNPase, dMBP, and GFAP were analyzed as the percentage area of positive staining (number of positive pixels/mm2) within the region of interest. Iba1, PDGFRα, BrdU, and OLIG2 were quantified as the density of cells in the region of interest (number of cells/mm2). LAMP1 and CD68 were analyzed as the percentage area of LAMP1+Iba1+ and CD68+Iba1+ staining (number of positive pixels/mm2) and then normalized on the percentage of Iba1+ staining (number of positive pixels/mm2) within the region of interest. For confocal analysis, images were acquired with an Olympus FV1200 laser scanning confocal microscope (Olympus-America Inc., Waltham, MA) equipped with a PlanApoN 60 , 1.4 NA super corrected oil objective. The Olympus FV1200 confocal microscope was equipped with five detectors: two spectral and one filter-based and two gallium arsenide phosphide (GaAsP) photo-multiplier tubes (PMTs). The 405-, 488-, and 559-nm diode lasers and 635-nm HeNe (helium neon) lasers were used with an optimal pinhole of 1 airy unit to acquire images. Images were finally processed with ImageJ and Imaris Software (Bitplane, Switzerland).
APP is Enriched in the Lysosome in Neuronal SN56 cells. SN56 cells were transiently co-transfected with fluorescent-tagged APP and compartment marker proteins and imaged using laser scanning confocal microscopy. A. SN56 cells were transiently co-transfected with the βAPP-CFP (shown in green) constructs along with compartment markers (red) as indicated demonstrating preferential co-localization of βAPP with lysosomal marker LAMP1. Colocalized pixels were identified as in figure 3 and displayed in the white colocalization channel. Scale Bar = 10 microns. B. The colocalization of the brightest 2% of pixels of APP and compartment markers was quantitated by Imaris software. Values are expressed as the mean SEM for a minimum of 50 cells each for Rab5, Rab7, Rab9 and LAMP1, and 20 cells for Cox8, drawn from at least 4 independent transfections. * indicates statistically significant difference from all other compartment markers (p