Computational protocol: How Variable Clones Build an Invariant Retina

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Protocol publication

[…] The cell number of entire retinas or individual cell types was formulated by multiplying the cell density by the volume of retinas (or individual cell layers). To measure the volume, we acquired the confocal z stacks of entire retinas at distinct stages (24, 32, 48, 52, and 72 hpf) on the inverted confocal microscope (Olympus FV1000) equipped with 40× oil objective (NA = 1.3). The surfaces of retinas were created based on retinal confocal stacks using the contouring adaptive tools in Imaris 7.3 (Bitplane). To distinguish different cell layers, we crossed the H2B-GPF line with the Ptf1a-DsRed line, in which all layers were separated in space by the Ptf1a-DsRed labeling and the surface of individual layers therefore could be reliably generated. The resultant surface was further used to calculate the volume using the statistics tool in Imaris 7.3.Cell density was estimated by counting the number of cells in given 1 μm sagittal section acquired using the confocal microscope (Olympus FV1000), at a depth in which all the cell layers were present, followed by a necessary correction using the protocol outlined in . Cell number in retina sections (or individual cell layers) was counted manually using ImageJ or Photoshop CS5 (Adobe), and the corresponding areas were measured using the contouring adaptive and statistics tools in Imaris 7.3. […]

Pipeline specifications

Software tools Imaris, ImageJ
Applications Laser scanning microscopy, Microscopic phenotype analysis
Organisms Danio rerio