Austin's Imaging Blog

COMPLETE FLUORESCENCE FILTER LIST FOR MICROSCOPY

Austin — Thu, 03 May 2012 15:13:14 +0000

This post will grow over time, but I’m posting this so that researchers and vendors have access to one single repository of filter info. Hopefully this will make all of our lives easier!

Definitions:

ET – Chroma name for a sputter coated filter.
Multiband – filter set which allows multiple channels to pass through it at the same time. i.e. viewing through the oculars on the scope will show you a multi-color image. NOT for use with monochrome cameras!
Pinkel – Set designed with individual exciter filters, with a single, multiband dichroic and emitter.
Sedat – Set designed with individual exciters and individual emitters, and a single multiband dichroic.
Zero Shift – Filter gued into cube and pre-aligned for multi cube acquisition use.

Tools

Semrock Searchlight tool for matching fluorophores and filters
Invitrogen / Molecular Probes SpectraViewer (Requires Java)
Chroma FluoroSRCH iOS/Android App for matching fluorophores and filters

Chroma Filters

Standard single band sets for use in a filter cube
ET single band sets for use in a filter cube
2 Channel Multiband sets for use in a cube
2 Channel Pinkel sets for use in a cube and a filter wheel
2 Channel Sedat sets for use in a cube and with two wheels
3 Channel Multiband sets for use in a cube
3 Channel Pinkel sets for use in a cube and a filter wheel
3 Channel Sedat sets for use in a cube and two wheels
4 Channel Pinkel sets for use in a cube and a filter wheel
4 Channel Sedat sets for use in a cube and two wheels
RGB Emission Set for Acquiring Color images with a monochrome camera

Semrock Filters

Standard single band sets for use in a filter cube
2 Channel Multiband sets for use in a cube
2 Channel Pinkel sets for use in a cube and a filter wheel
2 Channel Sedat sets for use in a cube and with two wheels
3 Channel Multiband sets for use in a cube
3 Channel Pinkel sets for use in a cube and a filter wheel
3 Channel Sedat sets for use in a cube and two wheels
4 Channel Multiband Sets for use in a cube
4 Channel Pinkel sets for use in a cube and a filter wheel
4 Channel Sedat sets for use in a cube and two wheels
5 Channel Pinkel sets for use in a cube and a filter wheel
5 Channel Sedat sets for use in a cube and two wheels
Zero-Shift Filters (All Types)

Laser Grade Filters (For TIRF and STORM)

Confocal Dichroics (For Spinning Disks Like the Yokagawa CSU Series)

Semrock CSU-X1 Dichroics

Empty Cubes for Specific Microscopes

Posting’s Been Light

Austin — Tue, 01 May 2012 01:54:29 +0000

I must apologize for my lack of posts – I’ve been traveling a lot these past few weeks for work. In my travels I’ve come across this exceptional timelapse montage from Shawn Reeder. He spent two years putting the shots together. Timelapse work is extremely difficult, and it takes a big investment on the photographer to care for the equipment, plan the shots, get to and stay on location. Shawn’s work is a testament to what can be done with this method!

Yosemite Range of Light from Shawn Reeder on Vimeo.

HDR Microphotography

Austin — Tue, 24 Apr 2012 14:41:49 +0000

One of the most overlooked capabilities possessed by digital capture is what can be accomplished by image processing after capture. In modern EMCCD cameras, some processing is done directly in the camera head. Simple adjustments like background correction or shading correction are well known, but more complex operations, like HDR , or High Dynamic Range processing, can dramatically enhance the information gleaned from a specimen. HDR has been used by professional and amateur photographers to overcome the lack of dynamic range in CCD and CMOS sensors, and there’s no reason it can’t be used on microscopes. Here are some good examples of how this can be done. NIS Elements has a built in option for capture and processing of HDR images in one operation. ImageJ can use an optional plugin as described here.

-Austin

Formulas for microscopy

Austin — Fri, 20 Apr 2012 22:31:15 +0000

I had a customer recently ask for these, and I thought I’d post them. These are from Nikon Inc. I’ll also have them on the resources page for reference. These include Useful magnification, Brightness Factor, Refractive Index, Depth of Field at Image Plane, Depth of Focus at Specimen Plane, Useful Magnification and Infinity Optics Formulas.

Formula Key

TRAINING DOCS FOR FIJI STANFORD COURSE TODAY

Austin — Tue, 17 Apr 2012 16:58:40 +0000

If you’re attending the training course on Fiji programming at Stanford, you can download the example files here.

Synergy Aircraft to offer Kickstarter Funding Round

Austin — Mon, 16 Apr 2012 14:23:42 +0000

Synergy Aircraft is making a push towards it’s next level of research in a composite blended wing/tail concept. They physics models show that the design should produce superior flight performance over several extremes of the envelope, i.e. low drag, but low stall speeds, good lift and good linear flow. They are saying Wednesday will be the launch of the kickstarter campaign. I’m curious to see how it’ll go!

NIS Elements v4 and Bio Formats in Fiji/ImageJ

Austin — Fri, 13 Apr 2012 21:48:20 +0000

I’ve been receiving reports that images saved using NIS Elements V4 are not always opening under the typical plugins used for Fiji and/or Image J. If you plan on running a big set of acquisitions I recommend testing a few images before moving forward. In the meantime saving or exporting to TIFF should be a decent workaround, although requiring a little bit more import work.

Confocal Microscopy Explained

Austin — Sat, 07 Apr 2012 04:10:03 +0000

Kurt did a great job on this comprehensive video which covers spinning disk and point scanning methods.

BIDC Seminar 5PM @ UCSF

Austin — Thu, 05 Apr 2012 14:46:11 +0000

I’ll be presenting today at the BIDC on “MacGyver Microscopy” at the UCSF Parnassus campus. Hope to see you there!

More from the UCSF 2012 Course – Last Day

Austin — Sat, 31 Mar 2012 21:22:16 +0000

Another excellent STORM image from the course: