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Af6000 software v3

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AF6000 Leica Software v3.1.0 is a software application designed for Leica laboratory equipment. The software provides core functionality to support various laboratory operations.

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Lab products found in correlation

Dmi6000b, by Leica (2 mentions) Dfc365 fx camera, by Leica (2 mentions) Dmi6000, by Leica (1 mentions) Dfc365fx, by Leica (1 mentions) Anti iba1, by Fujifilm (1 mentions) Paraformaldehyde (pfa), by Thermo Fisher Scientific (1 mentions)

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AF6000 (157 citations)

3 protocols using af6000 software v3

1

Detailed iPSC-Derived Neuron Imaging

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All fluorescence signals for iPSC-derived neurons were imaged with a Leica DMI 6000 inverted fluorescent microscope equipped with APO 63X/ 1.4 NA oil immersion lens and a filter set for fluorophores in Cy3, Cy5, GFP, and DAPI channels (center/ band width, nm: EX 545/39, 620/60, 470/40, 360/40; EM 605/75, 700/75, 525/45, 470/40). Images were collected with Leica DFC365 FX camera (6.45 μm pixel size) using AF6000 Leica Software v3.1.0 (Leica Microsystems). Whole cell, 12-bit stacks images with 0.2 μm step size were acquired (50–70 planes). Immersion oil (Leica, 11513859) with 1.518 refractive index at room temperature was applied to the lens. Coverslips were mounted with ProLong Gold anti-face reagent (Invitrogen, P36930) with a refractive index of 1.46. All images were acquired with identical microscope settings within individual experiments. Brightness and contrast were adjusted equally for all images and cropped insets were generated in the same manner among all the experiments to facilitate visualization of representative cells. For any image adjustment, identical settings were always applied to all cells, irrespective of genotype. Neurons that were clumped, overlapping or obscured by debris were excluded from the quantification.
Lin Y.C., Kumar M.S., Ramesh N., Anderson E.N., Nguyen A.T., Kim B., Cheung S., McDonough J.A., Skarnes W.C., Lopez-Gonzalez R., Landers J.E., Fawzi N.L., Mackenzie I.R., Lee E.B., Nickerson J.A., Grunwald D., Pandey U.B, & Bosco D.A. (2021). Interactions between ALS-linked FUS and nucleoporins are associated with defects in the nucleocytoplasmic transport pathway. Nature neuroscience, 24(8), 1077-1088.
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2

Fluorescence Imaging of Cellular Samples

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Cells were imaged under APO 63X/ 1.4 NA oil immersion lens using a Leica DMI 6000B inverted fluorescent microscope fitted with Leica DFC365 FX camera (6.45 μm pixel size). The immersion oil (Leica, 11513859) has a refractive index of 1.518 at ambient temperature. Fluorescence was detected using Cy3, Cy5, GFP, and DAPI channels (center/ bandwidth, nm: EX 545/39, 620/60, 470/40, 360/40; EM 605/75, 700/75, 525/45, 470/40). Images with a 0.2 μm step size were acquired (15–20 planes) using AF6000 Leica Software v3.1.0 (Leica Microsystems), and maximum projections of the center 5 planes were generated. Within each experiment, all the images were acquired using identical microscope settings.
Kumar M.S., Stallworth K.M., Murthy A.C., Lim S.M., Li N., Jain A., Munro J.B., Fawzi N.L., Lagier-Tourenne C, & Bosco D.A. (2023). Interactions between FUS and the C-terminal domain of Nup62 are sufficient for their co-phase separation into amorphous assemblies. Journal of molecular biology, 435(6), 167972.
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3

Immunofluorescence Analysis of iPSC-derived Macrophages

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iPSC-derived macrophages plated on coverslips were fixed with 4% paraformaldehyde (Fisher Scientific) and processed for immunofluorescence analysis as detailed previously.106 (link) Cells were incubated in a rabbit anti-IBA1 (1:1000, Wako Chemicals) primary antibody.
Immunofluorescence images were collected with a Leica DMI 6000B inverted fluorescent microscope using a 40X air objective and Leica DFC365 FX camera with AF6000 Leica Software v3.1.0 (Leica Microsystems). Stacked images (z=0.2μm) were maximum projected. Brightness and contrast were equally adjusted post-acquisition to improve visualization of fluorescent signals. Brightfield images were acquired on live cells using an EVOS ci inverted microscope (AMG) with 4x and 10x objectives. (Figure S6J).
Pantazis C.B., Yang A., Lara E., McDonough J.A., Blauwendraat C., Peng L., Oguro H., Kanaujiya J., Zou J., Sebesta D., Pratt G., Cross E., Blockwick J., Buxton P., Kinner-Bibeau L., Medura C., Tompkins C., Hughes S., Santiana M., Faghri F., Nalls M.A., Vitale D., Ballard S., Qi Y.A., Ramos D.M., Anderson K.M., Stadler J., Narayan P., Papademetriou J., Reilly L., Nelson M.P., Aggarwal S., Rosen L.U., Kirwan P., Pisupati V., Coon S.L., Scholz S.W., Priebe T., Öttl M., Dong J., Meijer M., Janssen L.J., Lourenco V.S., van der Kant R., Crusius D., Paquet D., Raulin A.C., Bu G., Held A., Wainger B.J., Gabriele R.M., Casey J.M., Wray S., Abu-Bonsrah D., Parish C.L., Beccari M.S., Cleveland D.W., Li E., Rose I.V., Kampmann M., Aristoy C.C., Verstreken P., Heinrich L., Chen M.Y., Schüle B., Dou D., Holzbaur E.L., Zanellati M.C., Basundra R., Deshmukh M., Cohen S., Khanna R., Raman M., Nevin Z.S., Matia M., Van Lent J., Timmerman V., Conklin B.R., Chase K.J., Zhang K., Funes S., Bosco D.A., Erlebach L., Welzer M., Kronenberg-Versteeg D., Lyu G., Arenas E., Coccia E., Sarrafha L., Ahfeldt T., Marioni J.C., Skarnes W.C., Cookson M.R., Ward M.E, & Merkle F.T. (2022). A reference human induced pluripotent stem cell line for large-scale collaborative studies. Cell stem cell, 29(12), 1685-1702.e22.
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