Bright field illuminationapp

As an alternative to CIDRE there is also BaSiC . There is an update site available for it and you can find a bit of demo/documentation here . If I remember correctly it does work on stacks and was quite fast.

Bright fieldmicroscope application

the BioVoxxel Pseudoflatfield correction with a radius around 10 also doesn´t look too bad and it´s super easy to use. There are some artifacts in the lower left corner which I guess are due to the jpeg format of the sample image.

If you have many images from the same microscope under similar settings, you can estimate the flatfield with CIDRE https://github.com/smithk/cidre.

Bright field illuminationpdf

CIDRE works really well! However I would need to write an other UI that enables batch-processing of many experiments and also accepts Tiff stacks as input. I guess it would make to use your new code as a starting point, rather than the original one?

Bright fieldmicroscope parts and functions

If you have more images than CDRE can digest or you’re interested in 3D flatfields (I gues you’re not ;)), you can use our not yet published scale up of the CIDRE approach https://github.com/saalfeldlab/stitching-spark.

to me it seems you need a flat-field correction. [https://en.wikipedia.org/wiki/Flat-field_correction] This means, you should divide by the correction, not subtract it (also the Fourier filters do a subtraction, not a division). Otherwise the features in the dark (insufficiently illuminated) parts of the image get too weak. You could try, e.g., the following macro:

I have now a similar dataset (a time-laps of 60 wells with 6x6 tiles per well in Brightfield) and it would be great if you would have code that I could use Thanks!

Bright-field microscope Diagram

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Just for the record (maybe other people will find this post interesting): CIDRE and BaSiC are giving very similar results for my data (just different treatment of the offset due to the particular CIDRE settings that I used): image2384×1478 1.06 MB

To successfully repair your broken fiber optic cable, you're going to need to collect some supplies before you start. These tools include:

The first thing you'll need to do is remove the damaged section from your cable. Cut your fiber optic cable using your cutter tool, severing enough to eliminate any sign of damage. The cut should be straight and clean on both sides to ensure a stronger connection when it's time to join the ends.

unfortunately you didn’t use the provided sample image for your experiments. Furthermore, the provided sample image is JPG-compressed …

PS: Here are again results obtained from the supplied sample image. Profiles are on the image diagonal from left bottom to right top.

Darkfieldmicroscope

As an alternative to CIDRE there is also BaSiC. There is an update site available for it and you can find a bit of demo/documentation here. If I remember correctly it does work on stacks and was quite fast.

Your new code (right?): https://github.com/saalfeldlab/stitching-spark/blob/42e01a6fe2751980102922513df309ba25b00f70/src/main/java/org/janelia/stitching/experimental/IlluminationCorrectionSliceParallel.java#L1452

Once you've identified and inspected the damage, you can get started with a few straightforward steps to fix your cable.

Integral images have been introduced in by Crow (1984)[1] as a technique to improve texture rendering speed at multiple scales in perspective projections. The technique has since then been used for a number of applications. The most popular...

While fiber optic cables are resilient to harsh wear and tear, they may experience damage over time. When this happens, it's crucial to understand what you can do to get your network back online to avoid costly delays and expensive repairs.

In fact, I do have more images. My naive approach was just to compute a median projection, thereby ideally removing the objects and only being left with the flat-field. This of course does not work very robustly if there are many objects in every image. Thus, thanks for pointing out CIDRE I will check it out!

Bright fieldmicroscope principle

In the case in question they zero out harmonic spatial waves of large periods. Division is the way to go but improved image acquisition is superior!

With the ends freshly trimmed, use your stripper to expose the optic fibers. Place the jaws of the stripper at the location you want to begin, squeezing the handle and pulling it toward the cut end to remove the outer coating.

Bright fieldmicroscope

I have now a similar dataset (a time-laps of 60 wells with 6x6 tiles per well in Brightfield) and it would be great if you would have code that I could use Thanks!

If you plan on using a mechanical splice, you can estimate how much you should trim by holding your metal terminal next to the end of the cable. It's wise to strip away enough of the coating so that the end reaches the tip of the terminal. You can use a similar tactic if you're using a fusion splice. Do this for both ends.

Could you please test it? Update site: EMBL-CBA And then at the very bottom of Plugins > Restoration > Illumination > BaSiC (I am not sure it will work immediately because I had some strange dependency issues…)

there are a few documented methods. From these, I found the FFT bandpass filter to work nice and fast, but the result using your image posted above is not necessarily of better quality compared to what you already have.

If you’re only after a band pass, you could also try Plugins > Integral Image Filters > Normalize Local Contrast which is even faster than the FFT bandpass. Try various block-sizes with preview checked

Once your splice is in place, there are some things you can do to ensure a secure connection. With a mechanical splice, you can perform a tug test, pulling on either end of the splice. Or, you can use an OTDR for more detailed information to test the strength of the signal, fixing any issues as needed.

What magnification? If overall magnification is small, a normal Microscope may be sub-optimum and special illumination may be needed.

I was wondering whether there is an ImageJ workflow already for correcting brightfield illumination? I just tried an own attempt (median filter based) and I guess that would be OK but I also do not want to reinvent the wheel…

It's crucial to thoroughly clean the cable before moving forward. Use alcohol and a lint-free cloth to wipe down the fiber. Tiny fibers on the core's surface can affect its performance, rendering it ineffective. Once clean, do not touch the ends of the fiber to preserve its integrity.