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Two separate microscope filters were prepared for each sample, and evaluated by 2 independent, experienced microscopists.
The red channel, used for mOrange, tdTomato, TagRFP and mRFP1.2, used a polychromator set at 550 nm, a 570DRLP beamsplitter, and a 595/40 nm emission filter placed in the filterwheel under the microscope (filters were obtained from Omega Optical).
Protein localization was determined using a Leica SP5 laser scanning confocal microscope (filters: 406 nm for DAPI, 488 nm for Fluor 488, and 543 nm for Fluor 568).
The images acquired with the different microscope filters for a given field were merged to obtain a single three coloured image, where blue always corresponded to the total cell nuclei that incorporated the Hoechst dye.
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"You take two pieces of fairly traditional technology [the laser and the microscope filtering lenses], and you put this fairly simple fiber-optic bundle in the middle, and all of a sudden you can scan 25 million cells a minute," Bruce says.
Appropriate IIF controls with no primary antibody revealed no detectable bleed-through between microscope filter sets.
Immunofluorescence was observed with appropriate microscope filter sets for Alexa Fluor-488, Alexa Fluor-594 and Cy3.
Dichroic filters designed to enhance machine vision devices were used because they are much less expensive than epifluorescent microscope filter sets.
Appropriate IIF controls with no or only one primary antibody or both secondary antibodies alone or in combination revealed no observable non-specific background staining and no detectable bleed-through between microscope filter sets.
Approximate respective excitation and emission wavelengths for the microscope filter sets used were 571 and 627 nm for Texas Red, 495 and 531 nm for FITC, 436 and 480 nm for DEAC, and 402 and 462 nm for DAPI.
This overlap does not reflect bleed-through between channels, as these were acquired sequentially and the microscope filter setup allowed clear separation of the utilized fluorophores (supplementary material Fig. S1C).
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