scanning microscope
The Virtual Microscope 6.2.2
The Virtual Microscope - supports interactive viewing of high-resolution, multi-dimensional datasets from various microscopes more>>
The Virtual Microscope is a tool that supports data from a Philips Environmental Scanning Electron Microscope (ESEM), and a Fluorescence Light Microscope.
Interface Controls
The interface provides a simulation of our actual microscope interface(s). Controls common to all datasets include brightness, magnification (usually up to 1800x), navigation, measurement, and annotation. SEM samples include a contrast control, and some also include a focus control.
The navigation and magnification controls allow the user to explore any point of interest on the sample. This differs from other virtual microscopes that have been produced which provide only a few hot spots that can be magnified and explored.
Focus
The focus control is a real focal plane adjustment instead of a blurring of the image. Our automated data capture software (see below) allows us to capture an arbitrary number of focal planes. Thus, the focus control on the Virtual Microscope allows the user to glide through those planes interactively, bringing items closer and farther into focus. This is particularly useful with thick specimens viewed in the SEM.
Annotations
We have included a full set of specimen annotation tools so that experts and laypeople alike can mark up the datasets for future reference. These annotations are useful for teaching details about the data, as well as for allowing teachers to ask students to identify data features as homework. The annotations can be saved and reloaded as XML files.
Automated Data Collection
It can take thousands of images to fully describe a single specimen so that the user can explore any point at varying magnifications with multiple focal planes. As a result, some our datasets are many gigabytes (GB) in size. In order to accurately and sanely collect this data, we have written various software programs that automatically control the instruments.
The Bugscope Connection
The software for our SEM is based off of a work on a previous project called Bugscope. Bugscope is an online educational outreach project that provides real-time access to our SEM over the web so that school children can look at bugs from their own backyards.
We have leveraged the remote-control software we wrote for Bugscope into an automated data-collection package for the SEM. On the Light Microscope, we are using Openlab, and will be distributing our tiling scripts in case you have a similar system.
Specimen IDs
Each Virtual Microscope specimen gets its own unique specimen identification number. For those building new samples, click the button below to generate a new specimen ID. Generated IDs expire after two months, so dont grab one until you need it. When specimens are submitted, we will verify they have a valid ID automatically.
Scan Again 1.0
Scan Again - A GUI front-end for SANE (Scanner Access Now Easy) more>>
These were originally developed for Linux, but work on other operating systems, including Mac OS X.
I had this problem with an HP scanner I picked up at a rummage sale, and was able to get it to work using SANE. The trouble was that the SANE utilities are all command-line, and I got tired of typing.
I decided to make a GUI shell to interface with the command-line utilities, and I did this using RealBasic .
The resulting program runs the command-line utilities for you. It searches for scanners, putting the results into a pop-up at the top of the window ( see screen shot ).
It then interrogates the selected scanner for available options, and populates the spinners and pop-ups with the options available for the given scanner.
Scan Lines 1.0.0
Scan Lines introduces artificial scan lines into the clip, making it appear like early-day computer graphics and arcade machine more>>
Use Scan Lines whenever you want to introduce some stylish, but otherwise not very useful scan line effects or other regular horizontal lines into your clip.
Main features:
- area of effect: define the area of the clip you want to be affected by the plug-in. all other parts or the clip remain untouched.
- line color: this specifies the color that the scan lines are drawn in.
- separation: this tells the plug how far apart the scan lines should be generated.
- thickness: this defines the thickness of the scan lines
- opacity: this slider controls how transparent the scan lines are.
ScanCalc 1.7
ScanCalc - Utility for calculating the size of scanned images more>>
This can be helpful if youre having a service bureau scan some slides for you and you need to know how many removable cartridges to send. Its also useful if youre concerned about image size and want to see the difference between scanning an image at 300 DPI versus 400 DPI.
ScanCalc also functions as a proportional wheel: enter in a new height or width and ScanCalc will show you the percentage of enlargement/reduction. ScanCalc works with several measurement systems, including inches, points, and metric.
Main features:
- Simple
- Handy log for recording multiple measurements
- Can memorize frequently used picture sizes.
Enhancements:
- Logging and favorite sizes were added.
Doublet Scan Lite 1.0
Doublet Scan Lite is a fast way to find all the duplicates, empty folders and unique files on your hard disks more>> Doublet Scan Lite is a fast way to find all the duplicates, empty folders and unique files on your hard disks. It s very easy to use: load the directory of your hard disks and scan for the duplicate files... after these two easy steps, you ll be able to select all the duplicate files you want to eliminate and move them to the trash.
PowerPC, MacOS 8.1 or later.
Canon Printer Drivers 2.2 for Mac OS X v10.6
Canon Printer Drivers is designed to appeal many users with the latest and helpful Canon printing and scanning software for Snow Leopard. more>>
Canon Printer Drivers 2.2 for Mac OS X v10.6 is designed to appeal many users with the latest and helpful Canon printing and scanning software for Snow Leopard.
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iAntiVirus 1.3.5
iAntiVirus offers you a reliable and useful protection and comprehensive system scanning to ensure your Mac remains safe and virus free. more>> iAntiVirus 1.3.5 offers you a reliable and useful protection and comprehensive system scanning to ensure your Mac remains safe and virus free.
Requirements: Mac OS X 10.5 or later.
hping2 2.0.0 RC3
Free command-line oriented TCP/IP packet assembler/analyzer more>> Free command-line oriented TCP/IP packet assembler/analyzer
hping2 is an interactive packet costructor and responses analyzer that uses the same CLI of the ping program (but with a lot of extensions).
hping2 can be used to performs a lot of tasks, like testing of firewall rules, (spoofed) port scanning, et cetera.
The interface is inspired to the ping(8) unix command, but hping isnt only able to send ICMP echo requests.
hping2 supports TCP, UDP, ICMP and RAW-IP protocols, has a traceroute mode, the ability to send files between a covered channel, and many other features.
hping2 is multi-platform and works on the following OSs: Mac OS X, Linux, FreeBSD, NetBSD, OpenBSD, Solaris, Windows.
Main features:
- Firewall testing
- Advanced port scanning
- Network testing, using different protocols, TOS, fragmentation
- Manual path MTU discovery
- Advanced traceroute, under all the supported protocols
- Remote OS fingerprinting
- Remote uptime guessing
- TCP/IP stacks auditing
- hping can also be useful to students that are learning TCP/IP.
Epson Scan to File 1.00E
Epson Scan to File is a distinguished and tractable application for Mac OS X that allows you to scan and save images from EPSON scanners. more>>
Epson Scan to File 1.00E is a distinguished and tractable application for Mac OS X that allows you to scan and save images from EPSON scanners.
b.scan 1.0.1
b.scan is an beneficial and easy to use file analyzer utility. more>>
b.scan 1.0.1 is an beneficial and easy to use file analyzer utility. It is designed for Mac developers to check binary files.
- analyze datafork of ANY file
- interpret any portion of data
- interpret as byte, short, integer, double, little and big endian
- display as hex, oct, decimal or character
Epson Scan Utility/TWAIN driver 2.77a
This file contains the EPSON Scan Utility and TWAIN Driver v2.77A for PowerPC Macs with OS X (v10.2.x or later) and Intel-based Macs with OS X (v10.4.4 or later) more>> This file contains the EPSON Scan Utility and TWAIN Driver v2.77A for PowerPC Macs with OS X (v10.2.x or later) and Intel-based Macs with OS X (v10.4.4 or later).
Mac OS X 10.2 or later.
Virex Folder Scan Scripts 1.0.1
Virex Folder Scan Scripts - AppleScript to autoscan downloaded files more>>
You can attach this script to multiple folders, I use my desktop and my Erage attachments folder.
Enhancements:
- added a file/folder size compare loop for the downloads. It compares file sizes every 3 seconds, and when they match, downloads done, scan. This is obviously not foolproof, especially on balky modem lines, but if need be, I can increase this. just email me, jwelch@mit.edu, and let me know.
scan.sh 1.0b1
scan.sh has come as an external filter for CommuniGatePro with which you can easily filter out emails with certain types of attachments based on file-extension (.exe .pif ...) more>>
scan.sh 1.0b1 has come as an external filter for CommuniGatePro with which you can easily filter out emails with certain types of attachments based on file-extension (.exe .pif ...)
SteveScan 2.0
SteveScan - Continue to use Virex 7 on systems incompatible with it, such as MacOS X Tiger more>>
Simply install Virex 7 and then disable all the background applications it installs. Do not use the Virex 7 application since it will enable all the background applications again.
Open SteveScan and run a scan. SteveScan can scan and disinfect the startup disk or users folder. It can also repair permissions and link you to the download site for Virex eupdates.
SteveScan has been tested with Virex 7.2.1, but should be compatible with Virex 7.5.1 as well.
Enhancements:
- User feedback while scanning.
- Scans can be canceled.
- Choose to scan the users folder or the startup disk.
- Faster GUI.
- Print reports.
- Save reports to a text file.
SAV Update 1.0
SAV Update is designed to be a script in which the auto-update feature for individual installations is not included. more>>
SAV Update 1.0 is designed to be a script in which the auto-update feature for individual installations is not included. This script downloads and installs the latest IDE files, then opens the SAV system preference to prompt the user to restart InterCheck scanning.