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Improves reader comparison:
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- measures memory footprint
- adds a summary table over all tested files
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NicoKiaru committed Aug 13, 2023
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4 changes: 3 additions & 1 deletion README.md
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A revamped version of the original ZeissCZIReader which parses faster the metadata. This is critical to open multi-TB files in Fiji in a reasonable amount of time.

This new reader is tested against a [list of publicly available CZI files](comparison_summary.md).

For more information see:
- the [original issue](https://github.com/ome/bioformats/issues/3839)
- a [draft PR on Bio-Formats](https://github.com/ome/bioformats/pull/4009)
- go to the compare folder of this repository to see how this readers differs from the bio-formats reader for a set of publicly available czi files

To use this reader instead of the original one, you will need to activate a Fiji update site, (not implemented yet)
To use this reader instead of the original one, you will need to activate the Fiji update site [Zeiss Quick Start Reader](https://imagej.net/plugins/zeiss-quick-start-reader) and by enabling the Zeiss(CZI) Quick Start reader in the Bio-Formats plugins configuration.

Special thanks to Zeiss for [opening its file format](https://github.com/ZEISS/libczi) and allowing open source software to improve!
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# [10.5 dpc vegfc gapdh Pecam wt 1.czi](https://zenodo.org/record/7430767/files/10.5%20dpc%20vegfc%20gapdh%20Pecam%20wt%201.czi) report
- **Autostitch** = false
- ZeissCZIReader v6.13.0
- ZeissQuickStartCZIReader v0.1.4-SNAPSHOT
- ZeissCZIReader v6.14.0
- ZeissQuickStartCZIReader v0.1.7-SNAPSHOT

# Images

| Series | Quick Start Reader | Size | Original Reader | Size |
|-------------------|--------------------|------|-----------------|------|
| Read time (all) |58 ms|------|61 ms|------|
| Read time (all) |68 ms|------|68 ms|------|
|0|![10.5 dpc vegfc gapdh Pecam wt 1.quick_true.flat_true.stitch_false.series_0.jpg](10.5 dpc vegfc gapdh Pecam wt 1/10.5 dpc vegfc gapdh Pecam wt 1.quick_true.flat_true.stitch_false.series_0.jpg)|X:512<br>Y:512<br>C:3<br>Z:1<br>T:1|![10.5 dpc vegfc gapdh Pecam wt 1.quick_false.flat_true.stitch_false.series_0.jpg](10.5 dpc vegfc gapdh Pecam wt 1/10.5 dpc vegfc gapdh Pecam wt 1.quick_false.flat_true.stitch_false.series_0.jpg)|X:512<br>Y:512<br>C:3<br>Z:1<br>T:1|

# Metadata

| Method | Parameters | Quick Start Reader | Original Reader | Delta |
| -------------------|------------------|--------------------|-----------------|------- |
| Initialization | |17 ms|17 ms| |
| Initialization | |20 ms|21 ms| |
| Reader Size (Mb) | |1.89|2.71| |
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# [10.5 dpc vegfc gapdh Pecam wt 1.czi](https://zenodo.org/record/7430767/files/10.5%20dpc%20vegfc%20gapdh%20Pecam%20wt%201.czi) report
- **Autostitch** = true
- ZeissCZIReader v6.13.0
- ZeissQuickStartCZIReader v0.1.4-SNAPSHOT
- ZeissCZIReader v6.14.0
- ZeissQuickStartCZIReader v0.1.7-SNAPSHOT

# Images

| Series | Quick Start Reader | Size | Original Reader | Size |
|-------------------|--------------------|------|-----------------|------|
| Read time (all) |55 ms|------|62 ms|------|
| Read time (all) |62 ms|------|71 ms|------|
|0|![10.5 dpc vegfc gapdh Pecam wt 1.quick_true.flat_true.stitch_true.series_0.jpg](10.5 dpc vegfc gapdh Pecam wt 1/10.5 dpc vegfc gapdh Pecam wt 1.quick_true.flat_true.stitch_true.series_0.jpg)|X:512<br>Y:512<br>C:3<br>Z:1<br>T:1|![10.5 dpc vegfc gapdh Pecam wt 1.quick_false.flat_true.stitch_true.series_0.jpg](10.5 dpc vegfc gapdh Pecam wt 1/10.5 dpc vegfc gapdh Pecam wt 1.quick_false.flat_true.stitch_true.series_0.jpg)|X:512<br>Y:512<br>C:3<br>Z:1<br>T:1|

# Metadata

| Method | Parameters | Quick Start Reader | Original Reader | Delta |
| -------------------|------------------|--------------------|-----------------|------- |
| Initialization | |18 ms|18 ms| |
| Initialization | |20 ms|20 ms| |
| Reader Size (Mb) | |1.89|2.71| |
9 changes: 5 additions & 4 deletions compare/2021-02-25-tulip_Airyscan.flat_true.stitch_false.md
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# [2021-02-25-tulip_Airyscan.czi](https://zenodo.org/record/4662053/files/2021-02-25-tulip_Airyscan.czi) report
- **Autostitch** = false
- ZeissCZIReader v6.13.0
- ZeissQuickStartCZIReader v0.1.4-SNAPSHOT
- ZeissCZIReader v6.14.0
- ZeissQuickStartCZIReader v0.1.7-SNAPSHOT

# Images

| Series | Quick Start Reader | Size | Original Reader | Size |
|-------------------|--------------------|------|-----------------|------|
| Read time (all) |53 ms|------|52 ms|------|
| Read time (all) |79 ms|------|132 ms|------|
|0|![2021-02-25-tulip_Airyscan.quick_true.flat_true.stitch_false.series_0.jpg](2021-02-25-tulip_Airyscan/2021-02-25-tulip_Airyscan.quick_true.flat_true.stitch_false.series_0.jpg)|X:1000<br>Y:1000<br>C:1<br>Z:21<br>T:1|![2021-02-25-tulip_Airyscan.quick_false.flat_true.stitch_false.series_0.jpg](2021-02-25-tulip_Airyscan/2021-02-25-tulip_Airyscan.quick_false.flat_true.stitch_false.series_0.jpg)|X:1000<br>Y:1000<br>C:1<br>Z:21<br>T:1|

# Metadata

| Method | Parameters | Quick Start Reader | Original Reader | Delta |
| -------------------|------------------|--------------------|-----------------|------- |
| Initialization | |4 ms|5 ms| |
| Initialization | |9 ms|9 ms| |
| Reader Size (Mb) | |0.13|0.22| |
| getStageLabelX| Image 0 | 0.000 um | -33280.500 um | 33280.500 um |
| getStageLabelY| Image 0 | 0.000 um | 1262.370 um | 1262.370 um |
| getStageLabelZ| Image 0 | 0.000 um | 705.839 um | 705.839 um |
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9 changes: 5 additions & 4 deletions compare/2021-02-25-tulip_Airyscan.flat_true.stitch_true.md
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# [2021-02-25-tulip_Airyscan.czi](https://zenodo.org/record/4662053/files/2021-02-25-tulip_Airyscan.czi) report
- **Autostitch** = true
- ZeissCZIReader v6.13.0
- ZeissQuickStartCZIReader v0.1.4-SNAPSHOT
- ZeissCZIReader v6.14.0
- ZeissQuickStartCZIReader v0.1.7-SNAPSHOT

# Images

| Series | Quick Start Reader | Size | Original Reader | Size |
|-------------------|--------------------|------|-----------------|------|
| Read time (all) |34 ms|------|45 ms|------|
| Read time (all) |47 ms|------|59 ms|------|
|0|![2021-02-25-tulip_Airyscan.quick_true.flat_true.stitch_true.series_0.jpg](2021-02-25-tulip_Airyscan/2021-02-25-tulip_Airyscan.quick_true.flat_true.stitch_true.series_0.jpg)|X:1000<br>Y:1000<br>C:1<br>Z:21<br>T:1|![2021-02-25-tulip_Airyscan.quick_false.flat_true.stitch_true.series_0.jpg](2021-02-25-tulip_Airyscan/2021-02-25-tulip_Airyscan.quick_false.flat_true.stitch_true.series_0.jpg)|X:1000<br>Y:1000<br>C:1<br>Z:21<br>T:1|

# Metadata

| Method | Parameters | Quick Start Reader | Original Reader | Delta |
| -------------------|------------------|--------------------|-----------------|------- |
| Initialization | |4 ms|5 ms| |
| Initialization | |7 ms|18 ms| |
| Reader Size (Mb) | |0.13|0.22| |
| getStageLabelX| Image 0 | 0.000 um | -33280.500 um | 33280.500 um |
| getStageLabelY| Image 0 | 0.000 um | 1262.370 um | 1262.370 um |
| getStageLabelZ| Image 0 | 0.000 um | 705.839 um | 705.839 um |
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Binary file not shown.
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# [2021-02-25-tulip_unprocessed-Airyscan.czi](https://zenodo.org/record/4662053/files/2021-02-25-tulip_unprocessed-Airyscan.czi) report
- **Autostitch** = false
- ZeissCZIReader v6.13.0
- ZeissQuickStartCZIReader v0.1.4-SNAPSHOT
- ZeissCZIReader v6.14.0
- ZeissQuickStartCZIReader v0.1.7-SNAPSHOT

# Images

| Series | Quick Start Reader | Size | Original Reader | Size |
|-------------------|--------------------|------|-----------------|------|
| Read time (all) |116 ms|------|156 ms|------|
| Read time (all) |1216 ms|------|929 ms|------|
|0|![2021-02-25-tulip_unprocessed-Airyscan.quick_true.flat_true.stitch_false.series_0.jpg](2021-02-25-tulip_unprocessed-Airyscan/2021-02-25-tulip_unprocessed-Airyscan.quick_true.flat_true.stitch_false.series_0.jpg)|X:1024<br>Y:1024<br>C:2<br>Z:21<br>T:32|![2021-02-25-tulip_unprocessed-Airyscan.quick_false.flat_true.stitch_false.series_0.jpg](2021-02-25-tulip_unprocessed-Airyscan/2021-02-25-tulip_unprocessed-Airyscan.quick_false.flat_true.stitch_false.series_0.jpg)|X:1024<br>Y:1024<br>C:2<br>Z:21<br>T:32|

# Metadata

| Method | Parameters | Quick Start Reader | Original Reader | Delta |
| -------------------|------------------|--------------------|-----------------|------- |
| Initialization | |14 ms|24 ms| |
| Initialization | |45 ms|59 ms| |
| Reader Size (Mb) | |0.64|1.35| |
| getStageLabelX| Image 0 | 0.000 um | -33280.500 um | 33280.500 um |
| getStageLabelY| Image 0 | 0.000 um | 1262.370 um | 1262.370 um |
| getStageLabelZ| Image 0 | 0.000 um | 705.839 um | 705.839 um |
Expand Down Expand Up @@ -510,6 +511,5 @@
| getPlanePositionX| Image 0 Plane 122 | 0.000 um | -33280.500 um | 33280.500 um |
| getPlanePositionY| Image 0 Plane 122 | 0.000 um | 1262.370 um | 1262.370 um |
| getPlanePositionZ| Image 0 Plane 122 | 3.548 um | 709.387 um | 705.839 um |
| getPlaneDeltaT| Image 0 Plane 123 | | 1: ome.units.quantity.Time: value[0.0], unit[s] stored as java.lang.Double| 2: null |

More than 500 differences.
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# [2021-02-25-tulip_unprocessed-Airyscan.czi](https://zenodo.org/record/4662053/files/2021-02-25-tulip_unprocessed-Airyscan.czi) report
- **Autostitch** = true
- ZeissCZIReader v6.13.0
- ZeissQuickStartCZIReader v0.1.4-SNAPSHOT
- ZeissCZIReader v6.14.0
- ZeissQuickStartCZIReader v0.1.7-SNAPSHOT

# Images

| Series | Quick Start Reader | Size | Original Reader | Size |
|-------------------|--------------------|------|-----------------|------|
| Read time (all) |135 ms|------|147 ms|------|
| Read time (all) |182 ms|------|172 ms|------|
|0|![2021-02-25-tulip_unprocessed-Airyscan.quick_true.flat_true.stitch_true.series_0.jpg](2021-02-25-tulip_unprocessed-Airyscan/2021-02-25-tulip_unprocessed-Airyscan.quick_true.flat_true.stitch_true.series_0.jpg)|X:1024<br>Y:1024<br>C:2<br>Z:21<br>T:32|![2021-02-25-tulip_unprocessed-Airyscan.quick_false.flat_true.stitch_true.series_0.jpg](2021-02-25-tulip_unprocessed-Airyscan/2021-02-25-tulip_unprocessed-Airyscan.quick_false.flat_true.stitch_true.series_0.jpg)|X:1024<br>Y:1024<br>C:2<br>Z:21<br>T:32|

# Metadata

| Method | Parameters | Quick Start Reader | Original Reader | Delta |
| -------------------|------------------|--------------------|-----------------|------- |
| Initialization | |16 ms|26 ms| |
| Initialization | |18 ms|32 ms| |
| Reader Size (Mb) | |0.64|1.35| |
| getStageLabelX| Image 0 | 0.000 um | -33280.500 um | 33280.500 um |
| getStageLabelY| Image 0 | 0.000 um | 1262.370 um | 1262.370 um |
| getStageLabelZ| Image 0 | 0.000 um | 705.839 um | 705.839 um |
Expand Down Expand Up @@ -510,6 +511,5 @@
| getPlanePositionX| Image 0 Plane 122 | 0.000 um | -33280.500 um | 33280.500 um |
| getPlanePositionY| Image 0 Plane 122 | 0.000 um | 1262.370 um | 1262.370 um |
| getPlanePositionZ| Image 0 Plane 122 | 3.548 um | 709.387 um | 705.839 um |
| getPlaneDeltaT| Image 0 Plane 123 | | 1: ome.units.quantity.Time: value[0.0], unit[s] stored as java.lang.Double| 2: null |

More than 500 differences.
9 changes: 5 additions & 4 deletions compare/20221019_MixedGrain.flat_true.stitch_false.md
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# [20221019_MixedGrain.czi](https://zenodo.org/record/7260610/files/20221019_MixedGrain.czi) report
- **Autostitch** = false
- ZeissCZIReader v6.13.0
- ZeissQuickStartCZIReader v0.1.4-SNAPSHOT
- ZeissCZIReader v6.14.0
- ZeissQuickStartCZIReader v0.1.7-SNAPSHOT

# Images

| Series | Quick Start Reader | Size | Original Reader | Size |
|-------------------|--------------------|------|-----------------|------|
| Read time (all) |57 ms|------|68 ms|------|
| Read time (all) |72 ms|------|91 ms|------|
|0|![20221019_MixedGrain.quick_true.flat_true.stitch_false.series_0.jpg](20221019_MixedGrain/20221019_MixedGrain.quick_true.flat_true.stitch_false.series_0.jpg)|X:1024<br>Y:1024<br>C:2<br>Z:27<br>T:1|![20221019_MixedGrain.quick_false.flat_true.stitch_false.series_0.jpg](20221019_MixedGrain/20221019_MixedGrain.quick_false.flat_true.stitch_false.series_0.jpg)|X:1024<br>Y:1024<br>C:2<br>Z:27<br>T:1|

# Metadata

| Method | Parameters | Quick Start Reader | Original Reader | Delta |
| -------------------|------------------|--------------------|-----------------|------- |
| Initialization | |4 ms|6 ms| |
| Initialization | |6 ms|8 ms| |
| Reader Size (Mb) | |0.15|0.27| |
| getStageLabelX| Image 0 | 0.000 um | 11657.500 um | 11657.500 um |
| getStageLabelY| Image 0 | 0.000 um | -1811.380 um | 1811.380 um |
| getStageLabelZ| Image 0 | 0.000 um | -564.588 um | 564.588 um |
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9 changes: 5 additions & 4 deletions compare/20221019_MixedGrain.flat_true.stitch_true.md
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@@ -1,20 +1,21 @@
# [20221019_MixedGrain.czi](https://zenodo.org/record/7260610/files/20221019_MixedGrain.czi) report
- **Autostitch** = true
- ZeissCZIReader v6.13.0
- ZeissQuickStartCZIReader v0.1.4-SNAPSHOT
- ZeissCZIReader v6.14.0
- ZeissQuickStartCZIReader v0.1.7-SNAPSHOT

# Images

| Series | Quick Start Reader | Size | Original Reader | Size |
|-------------------|--------------------|------|-----------------|------|
| Read time (all) |52 ms|------|60 ms|------|
| Read time (all) |68 ms|------|80 ms|------|
|0|![20221019_MixedGrain.quick_true.flat_true.stitch_true.series_0.jpg](20221019_MixedGrain/20221019_MixedGrain.quick_true.flat_true.stitch_true.series_0.jpg)|X:1024<br>Y:1024<br>C:2<br>Z:27<br>T:1|![20221019_MixedGrain.quick_false.flat_true.stitch_true.series_0.jpg](20221019_MixedGrain/20221019_MixedGrain.quick_false.flat_true.stitch_true.series_0.jpg)|X:1024<br>Y:1024<br>C:2<br>Z:27<br>T:1|

# Metadata

| Method | Parameters | Quick Start Reader | Original Reader | Delta |
| -------------------|------------------|--------------------|-----------------|------- |
| Initialization | |4 ms|4 ms| |
| Initialization | |5 ms|6 ms| |
| Reader Size (Mb) | |0.15|0.27| |
| getStageLabelX| Image 0 | 0.000 um | 11657.500 um | 11657.500 um |
| getStageLabelY| Image 0 | 0.000 um | -1811.380 um | 1811.380 um |
| getStageLabelZ| Image 0 | 0.000 um | -564.588 um | 564.588 um |
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9 changes: 5 additions & 4 deletions compare/20221019_MixedGrain2.flat_true.stitch_false.md
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@@ -1,20 +1,21 @@
# [20221019_MixedGrain2.czi](https://zenodo.org/record/7260610/files/20221019_MixedGrain2.czi) report
- **Autostitch** = false
- ZeissCZIReader v6.13.0
- ZeissQuickStartCZIReader v0.1.4-SNAPSHOT
- ZeissCZIReader v6.14.0
- ZeissQuickStartCZIReader v0.1.7-SNAPSHOT

# Images

| Series | Quick Start Reader | Size | Original Reader | Size |
|-------------------|--------------------|------|-----------------|------|
| Read time (all) |28 ms|------|43 ms|------|
| Read time (all) |35 ms|------|53 ms|------|
|0|![20221019_MixedGrain2.quick_true.flat_true.stitch_false.series_0.jpg](20221019_MixedGrain2/20221019_MixedGrain2.quick_true.flat_true.stitch_false.series_0.jpg)|X:620<br>Y:620<br>C:2<br>Z:51<br>T:1|![20221019_MixedGrain2.quick_false.flat_true.stitch_false.series_0.jpg](20221019_MixedGrain2/20221019_MixedGrain2.quick_false.flat_true.stitch_false.series_0.jpg)|X:620<br>Y:620<br>C:2<br>Z:51<br>T:1|

# Metadata

| Method | Parameters | Quick Start Reader | Original Reader | Delta |
| -------------------|------------------|--------------------|-----------------|------- |
| Initialization | |4 ms|5 ms| |
| Initialization | |6 ms|7 ms| |
| Reader Size (Mb) | |0.18|0.34| |
| getStageLabelX| Image 0 | 0.000 um | 4905.320 um | 4905.320 um |
| getStageLabelY| Image 0 | 0.000 um | -69.713 um | 69.713 um |
| getStageLabelZ| Image 0 | 0.000 um | -540.459 um | 540.459 um |
Expand Down
9 changes: 5 additions & 4 deletions compare/20221019_MixedGrain2.flat_true.stitch_true.md
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@@ -1,20 +1,21 @@
# [20221019_MixedGrain2.czi](https://zenodo.org/record/7260610/files/20221019_MixedGrain2.czi) report
- **Autostitch** = true
- ZeissCZIReader v6.13.0
- ZeissQuickStartCZIReader v0.1.4-SNAPSHOT
- ZeissCZIReader v6.14.0
- ZeissQuickStartCZIReader v0.1.7-SNAPSHOT

# Images

| Series | Quick Start Reader | Size | Original Reader | Size |
|-------------------|--------------------|------|-----------------|------|
| Read time (all) |25 ms|------|33 ms|------|
| Read time (all) |31 ms|------|44 ms|------|
|0|![20221019_MixedGrain2.quick_true.flat_true.stitch_true.series_0.jpg](20221019_MixedGrain2/20221019_MixedGrain2.quick_true.flat_true.stitch_true.series_0.jpg)|X:620<br>Y:620<br>C:2<br>Z:51<br>T:1|![20221019_MixedGrain2.quick_false.flat_true.stitch_true.series_0.jpg](20221019_MixedGrain2/20221019_MixedGrain2.quick_false.flat_true.stitch_true.series_0.jpg)|X:620<br>Y:620<br>C:2<br>Z:51<br>T:1|

# Metadata

| Method | Parameters | Quick Start Reader | Original Reader | Delta |
| -------------------|------------------|--------------------|-----------------|------- |
| Initialization | |4 ms|5 ms| |
| Initialization | |8 ms|8 ms| |
| Reader Size (Mb) | |0.18|0.34| |
| getStageLabelX| Image 0 | 0.000 um | 4905.320 um | 4905.320 um |
| getStageLabelY| Image 0 | 0.000 um | -69.713 um | 69.713 um |
| getStageLabelZ| Image 0 | 0.000 um | -540.459 um | 540.459 um |
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9 changes: 5 additions & 4 deletions compare/Airyscan Lines Pattern.flat_true.stitch_false.md
Original file line number Diff line number Diff line change
@@ -1,20 +1,21 @@
# [Airyscan Lines Pattern.czi](https://zenodo.org/record/6848342/files/Airyscan%20Lines%20Pattern.czi) report
- **Autostitch** = false
- ZeissCZIReader v6.13.0
- ZeissQuickStartCZIReader v0.1.4-SNAPSHOT
- ZeissCZIReader v6.14.0
- ZeissQuickStartCZIReader v0.1.7-SNAPSHOT

# Images

| Series | Quick Start Reader | Size | Original Reader | Size |
|-------------------|--------------------|------|-----------------|------|
| Read time (all) |48 ms|------|42 ms|------|
| Read time (all) |71 ms|------|78 ms|------|
|0|![Airyscan Lines Pattern.quick_true.flat_true.stitch_false.series_0.jpg](Airyscan Lines Pattern/Airyscan Lines Pattern.quick_true.flat_true.stitch_false.series_0.jpg)|X:1000<br>Y:1000<br>C:1<br>Z:1<br>T:1|![Airyscan Lines Pattern.quick_false.flat_true.stitch_false.series_0.jpg](Airyscan Lines Pattern/Airyscan Lines Pattern.quick_false.flat_true.stitch_false.series_0.jpg)|X:1000<br>Y:1000<br>C:1<br>Z:1<br>T:1|

# Metadata

| Method | Parameters | Quick Start Reader | Original Reader | Delta |
| -------------------|------------------|--------------------|-----------------|------- |
| Initialization | |5 ms|6 ms| |
| Initialization | |7 ms|9 ms| |
| Reader Size (Mb) | |0.12|0.19| |
| getStageLabelX| Image 0 | 0.000 um | -10942.200 um | 10942.200 um |
| getStageLabelY| Image 0 | 0.000 um | -2472.760 um | 2472.760 um |
| getStageLabelZ| Image 0 | | 1: null| 2: ome.units.quantity.Length: value[-100.063], unit[µm] stored as java.lang.Double |
Expand Down
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