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The main disadvantage of high resolution microscopes is the short working distance between the objective and a specimen, especially at high magnifications (about 0.3 mm with 100× objective). As a result partially decapsulated chips cannot be observed and full decapsulation of the die is required. Using microscopes with a long working distance, for example the Mitutoyo FS70 [121] with 13 mm working distance on 200× objective, helps solve this problem but at a cost: the resolution is at most 0.4 µm because the NA cannot be high.
Another problem of the high-resolution objectives is a very short depth of focus, which makes the out-of-focus planes look blurred, thus reducing the image quality. This is more noticeable on multilayer chips where the distance between the top and the bottom layer is more than 1 µm.
Confocal microscopy reduces this effect as all out-of-focus planes become dark or appear in different colours depending from their depth. Such confocal systems are very expensive, especially the ones that use laser scanning, and therefore can be afforded by relatively large labs only. Even second-hand confocal microscopes start from £10,000.