Zen desk software

Manufactured by Zeiss

Sourced in Germany

Zen Desk Software is a digital imaging software platform developed by Zeiss for use with their microscopy equipment. The software provides tools for image acquisition, processing, and analysis. It serves as the primary interface for controlling and operating Zeiss microscopes.

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Lab products found in correlation

Lsm image software, by Zeiss (3 mentions) Lsm 710 meta inverted confocal microscope, by Zeiss (3 mentions) Dapi fluoromount g, by Thermo Fisher Scientific (2 mentions) Alexa fluor conjugated secondary antibody, by Thermo Fisher Scientific (2 mentions) Nunc lab tek chamber slide, by Thermo Fisher Scientific (1 mentions) Ci m6pr, by Abcam (1 mentions) Gm130, by BD (1 mentions)

4 protocols using zen desk software

Immunostaining of Postnatal Mouse Skin Fibroblasts

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Primary fibroblasts isolated from 1–2-day postnatal mouse skin were cultured on eight-well Nunc™ Lab-Tek™ Chamber Slide from Thermo Fischer. The cells were washed two to three times with PBS then fixed and permeabilized using 100% ice-cold methanol. After blocking with 10% normal goat serum, the cells were incubated with primary antibodies overnight at 4°C followed by Alexa Fluor- conjugated secondary antibodies (Life Technologies (Thermo Fisher Scientific) (dilution 1:1000) for 1 h at room temperature. The primary antibodies used were IP3 Receptor 1 (D53A5) (Cell Signaling, 8568S; Lot# 1 dilution 1:200), LAMP2 (Abcam, ab13524; Lot# GR3221693–4; Dilution 1:500), NFATC4 (Abcam, ab62613; Lot# GR70691–12; dilution1:500), LC3B (ab51520; dilution 1:200). Cells were mounted using DAPI-Fluoromount G (Thermo Fisher, 010020) and fluorescence was visualized with the Zeiss LSM 710 Inverted Meta confocal microscope (Carl Zeiss). The images were processed with the LSM Image Software (Carl Zeiss). Mender’s (colocalization coefficient was calculated using the Zen Desk Software from Zeiss.

Mondal A., Appu A.P., Sadhukhan T., Bagh M.B., Previde R.M., Sadhukhan S., Stojilkovic S., Liu A, & Mukherjee A.B. (2022). Ppt1-deficiency dysregulates lysosomal Ca++-homeostasis contributing to pathogenesis in a mouse model of CLN1 disease. Journal of inherited metabolic disease, 45(3), 635-656.

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Morphological Examination of Intestinal Villi and Crypts

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For the morphological examination, staining with hematoxylin and eosin was completed for visualization of villi and crypts. Intact villi with belonging crypts were examined for each slide with ZEN desk software (ZEISS, Oberkochen, Germany). Villus height (VH), villus width (VW), and crypt depth (CD) were measured by the measurement tools in the ZEN desk software, and the ratio of VH to CD was calculated using the former examinations. All 96 slides were investigated, and all intact villi were measured. The average number of villi per pig (three slides) was 13, and the total number of villi in each treatment group was 212 and 218, respectively.

Grove S.S., Dall J, & Madsen J.G. (2024). The Effect of Lysophospholipids and Sex on Growth Performance and Small Intestine Morphology in Weanling Pigs, 7–30 kg. Animals : an Open Access Journal from MDPI, 14(8), 1213.

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Immunofluorescence Staining of Primary Neurons

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Primary Neurons isolated from P2 pups were cultured on chamber slides for 7 days in Neurobasal media containing B27 supplement. The cells were then washed two to three times with PBS, incubated at 37 °C and fixed using 4% paraformaldehyde or 100% methanol (in −20 °C for 15 min). Paraformaldehyde-fixed cells were permeabilized with 0.1% Triton X-100 in PBS. After blocking with 10% normal goat serum, the cells were incubated with primary antibodies (Table 1) overnight at 4 °C. The cells were then washed with PBS and incubated with Alexa Fluor–conjugated secondary antibodies (Life Technologies, Thermo Fisher Scientific) for 1 h at room temperature. Cells were mounted using 4',6-diamidino--2-phenylindole-fluoromount G (Thermo Fisher Scientific, 010020), and fluorescence was visualized with the Zeiss LSM 710 Inverted Meta confocal microscope (Carl Zeiss). The images were processed with the LSM image software (Carl Zeiss). Overlap colocalization coefficient was calculated using Zen Desk software from Zeiss (104 (link)). We have used the weighted colocalization coefficient for analysis.

Bagh M.B., Appu A.P., Sadhukhan T., Mondal A., Plavelil N., Raghavankutty M., Supran A.M., Sadhukhan S., Liu A, & Mukherjee A.B. (2024). Disruption of lysosomal nutrient sensing scaffold contributes to pathogenesis of a fatal neurodegenerative lysosomal storage disease. The Journal of Biological Chemistry, 300(2), 105641.

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Lysosomal Protein Localization in CLN3 Fibroblasts

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Fibroblasts from CLN3 patients and age- and sex matched normal control subjects were cultured in 8 well chamber slides with DMEM washed 2 to 3 times with PBS and cells were fixed using 100% methanol. Then the cells were washed with PBS and blocked with 10% normal goat serum for 1 h., the cells were incubated with primary antibodies overnight at 4°C for 1 h at room temperature. The primary antibodies used were: Ppt1 (a gift from Dr. S.L. Hofmann; Dilution 1:1000), CIM6PR (Abcam, Cat #ab124767; Dilution 1:1000), LAMP2 (EMD Millipore; Cat #MABC40; Dilution 1:200) GM-130 (BD Biosciences, Cat #610823; Dilution 1:1,500), V0a1 (Abnova; Cat #H00000535-A01; Dilution 1:100), Na⁺ K⁺ ATPase (Cell Signaling, Cat#3010S; dilution 1:200) followed by Alexa Fluor-conjugated secondary antibodies (Invitrogen). Cells were mounted using DAPI-Fluoromount G (Thermo Fisher, 010020) and fluorescence was visualized with the Zeiss LSM 710 Inverted Meta confocal microscope (Carl Zeiss). Each experiment was repeated at least 3 times with 10 cells analysed per experiment per group (Total 30 cells per group). The image was processed with the LSM Image Software (Carl Zeiss 710) and Pearson’s colocalization coefficient (Dunn et al. 2011 (link)) was calculated (Dunn et al. 2011 (link)) using the Zen Desk Software from Zeiss.

Appu A.P., Bagh M.B., Sadhukhan T., Mondal A., Casey S, & Mukherjee A.B. (2019). Cln3-mutations underlying juvenile NCL cause significantly reduced levels of Ppt1-protein and Ppt1-enzyme activity in the lysosome. Journal of inherited metabolic disease, 42(5), 944-954.

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